Leica PELORIS, PELORIS II User Manual

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Leica PELORIS Leica PELORIS II

Rapid Tissue Processor

User Manual

™

Living up to Life

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Legal Notices

Intended Use Statement

The Peloris™ dual retort rapid tissue processor prepares tissue samples for sectioning by transforming fixed samples into wax embedded samples. This is achieved by exposing the tissue samples to a sequence of reagents in the processing retorts.

Trademarks

Leica and the Leica logo are registered trademarks of Leica Microsystems IR GmbH and used under license.

PELORIS, PELORIS II, Waxsol, Parablocks, ActivFlo and RemoteCare are trademarks of Leica Biosystems Melbourne Pty Ltd ACN 008 582 401. Other trademarks are the property of their owners.

Leica Biosystems Melbourne Pty Ltd owns the copyright on this document and any associated software.

Leica Biosystems Melbourne is part of the Leica Microsystems group of companies. Under law, our written permission is required before either the documentation or the software is copied, reproduced, translated, or converted to electronic or other machine-readable form, in whole or in part.

Doc. 26.7501.500 Rev K © Leica Biosystems Melbourne Pty Ltd 2011

Manufacturer

Leica Biosystems Melbourne Pty Ltd 495 Blackburn Rd Mt. Waverley VIC 3149 Australia

Important Information for All Users

Persons operating the Peloris tissue processor MUST:

 Follow the instructions for use exactly as described in this user manual. Any deviation from the

instructions may result in sub-optimal tissue processing, potential loss of the patient sample and the consequent inability to make a diagnosis.

 Receive sufficient training to ensure that the instrument is used in accordance with this user manual.

 Be aware of any potential hazards or hazardous procedures before operating the instrument as described

in this user manual.

Warranty claims can be made only if the system has been used for the specified application and operated according to the instructions in this document. Damage resulting from inappropriate handling and/or misuse of the product will invalidate the warranty. Leica Microsystems cannot assume liability for any such damage.

Due to a policy of continuous improvement, Leica Microsystems reserves the right to change specifications without notice.

Only trained staff are to remove any covers or parts from the processor, and only if instructed within this manual. Repairs must only be carried out by qualified service personnel authorized by Leica Microsystems.

The term “Leica Microsystems” when used in text in this document refers to Leica Biosystems Melbourne Pty Ltd.

The term “Peloris” when used in text in this document refers to Peloris and Peloris II.

Revision Record

Rev. Issued Detail

K02 July 2011 Updates to Important Information for All Users and Safety Notices

Section 5.1.5 Tissue Marking added. Chapter 9 "Troubleshooting" added.

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Contacting Leica Microsystems

For service or support contact your local representative or see www.leica-microsystems.com.

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Software Licence Terms

1 Defined terms & interpretation

1.1 Defined terms

In this agreement:

“Leica Microsystems” includes Vision BioSystems Pty Ltd ACN 008 582 401, prior to changing its company name, and Leica Biosystems Melbourne Pty Ltd ACN 008 582 401 after changing its name.

“Confidential Information” means all information:

(a) treated by Leica Microsystems as confidential or of its nature confidential; and

(b) disclosed by Leica Microsystems to the Licensee or of which the other party becomes aware,

except information:

(d) that is public knowledge (otherwise than as a result of a breach of confidentiality by the Licensee or any of its

permitted disclosees).

“Designated Computer” means the computer or microprocessor controlled unit supplied by Leica Microsystems to the Licensee under the Supply Agreement or otherwise recommended for use by Leica Microsystems.

“Documentation” means the manuals, user documentation, proprietary notices, product catalog, website notices and bulletins generally supplied by Leica Microsystems with or relating to the Software.

“Effective Date” means the date the Goods, as defined in the Supply Agreement, are delivered by Leica Microsystems.

“Intellectual Property” means all existing and future intellectual property rights including:

(e) patents, copyright (including all copyright and software), software and associated documentation including the

specific design and structure of individual programs, registered designs, trade marks, proprietary documentation and notices, and any right to have information or know-how kept confidential; and

(f) any application or right to apply for registration of any of the rights referred to in paragraph (e) above.

“Licensee” means the Purchaser or lessee of the Goods containing the Software, or, where the Licensee is a distributor of the Goods containing the Software, the end user of the Goods containing the Software.

“Licensor IP” means all Intellectual Property relating to:

(a) the Software and Documentation; (b) any modifications, upgrades, new versions or new releases of the materials referred to in paragraph (a) above; and

“Release” means each release of a new Version of the Software.”

“Software” means any program, firmware or electronic files that provides instructions or data to a computer or microprocessor and, shall for the purposes of this agreement, include original versions, modified versions, upgrades, updates, bug fixes, and backup copies.

“Supply Agreement” means the agreement between the Licensee and Leica Microsystems, or where the Licensee is not a direct customer of Leica Microsystems, between Leica Microsystems’ distributor and Leica Microsystems, for the sale, lease or use of the Goods.

“Third Party Material” means any Material owned by a third party that is not a Related Body Corporate (as that term is defined in the Corporations Act 2001 (Cth)) of Leica Microsystems.

1.2 Other definitions

In this agreement, “Goods”, “Purchaser”, and “Leica Microsystems” have the same meaning as in the Supply Agreement.

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Software Licence Terms

2 Grant of licence

2.1 Licensee gives consent

The Licensee agrees to be bound by all the terms of this Licence by downloading or installing the Software, or by agreeing to purchase, lease or otherwise use the Software or the Goods containing the Software.

2.2 Leica Microsystems grants licence

Subject to this agreement, Leica Microsystems grants the Licensee a non-transferable, non-exclusive licence to use the Software and Documentation for its internal business purposes in accordance with the terms of this agreement.

3Restrictions on use

The Licensee must:

(a) only use the Software on the Designated Computer and in conformity with:

(i) laboratory practices that are consistent with industry practice;

(ii) all applicable laws, regulations, guidelines and decisions of judicial or regulatory bodies;

(iii) any patent or other proprietary rights of third parties; and

(iv) as envisaged by the Documentation, and this agreement;

(b) not install, or procure the installation of, any software on the Designated Computer without Leica Microsystems' prior

written consent;

copied (other than one copy of the Software for backup purposes), without obtaining Leica Microsystems' prior written permission;

(d) not publish, distribute or commercialise all or part of the Software or Documentation, or any adaptation, modification

or derivative of the Software or Documentation;

(e) not sell, rent, lease, sub-license, assign or transfer all or part of the Software or Documentation or any of its rights

under this agreement;

(f) not use the Software or the Documentation for the benefit of any third party, or disclose the Software or the

Documentation to any third party, except with Leica Microsystems' prior written consent;

(g) not adapt, reverse engineer, make error corrections, or otherwise modify the Software or Documentation or create

derivative works based on the Software or Documentation (other than to the extent permitted by applicable copyright laws) or permit third parties to do the same;

(h) not decompile, decrypt, reverse engineer, disassemble or otherwise reduce the Software to human readable form to

gain access to trade secrets or confidential information in the Software or permit third parties to do the same; and

(i) comply with any reasonable directions of Leica Microsystems from time to time in relation to the installation or use of

the Software and the Documentation.

4 Intellectual property

4.1 Licensor IP

All Licensor IP, including but not limited to any images, audio, video and text in the Software, is owned by or licensed to Leica Microsystems, and no Licensor IP is transferred to the Licensee under this agreement.

4.2 Proprietary markings

The Licensee must not alter or remove any notices of proprietary rights, any rights management information or any serial numbers appearing on, attached to or incorporated in Licensor IP or any copies thereof, and must not use or attempt to register any trademark, trade name, business name or company name which is confusingly similar to any trademark or trade name of Leica Microsystems.

4.3 Violations of intellectual property

The Licensee must:

(a) notify Leica Microsystems immediately if it knows of or suspects any unauthorised use, or violation, of any Licensor

IP; and

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Software Licence Terms

(b) provide promptly, at its cost, all assistance reasonably requested by Leica Microsystems to protect the relevant rights

in Licensor IP and prosecute any claims arising from such uses or violations.

4.4 Compliance

The Licensee must comply, at all times, with any terms and conditions relating to the Third Party Material notified to the Licensee by Leica Microsystems and/or the third party supplier of that Third Party Material.

5 Upgrades and support

5.1 New releases and new versions

Leica Microsystems may, at its sole discretion, provide the Licensee with new Releases or new Versions of the Software.

5.2 Installation

If requested by the Licensee to do so, Leica Microsystems, its designated distributor or agent may, at its sole discretion, install a new Release or new Version of the Software on the Designated Computer.

5.3 Downloading of data

Leica Microsystems, or its designated agent may, at its sole discretion, download data that has been generated by the use of the Software by the Licensee as a means of debugging Software faults and otherwise analyzing the performance of the Software or Goods containing the Software supplied by Leica Microsystems under the Supply Agreement.

6 Back up and security of data

It is the Licensee's responsibility to:

(a) perform regular backups of data and to store these; and

(b) provide contingency plans for the event of a failure of any sort (eg: fire, flood, and theft);

and Leica Microsystems has no liability (including for negligence) for any loss whether direct or indirect, that could have been prevented by the Licensee performing the above responsibilities, or which occurs as a consequence of inadequate back up, computer viruses or the ongoing functions of computer hardware (including backup hardware), whether supplied by Leica Microsystems or any other supplier.

7 Confidentiality and privacy

7.1 Use and disclosure

The Licensee must, in relation to the Confidential Information:

(a) keep it confidential;

(b) use it only as permitted under this agreement and only disclose it:

(i) to employees, contractors and agents that have a need to know and who have undertaken to comply with this

clause 7; or

(ii) to the extent (if any) the Licensee is required by law to do so; and

required by law to be retained.

7.2 Recipient's obligations

The Licensee must:

(a) safeguard the Confidential Information from unauthorised access or use; and

(b) notify Leica Microsystems of, and take all steps to prevent or stop, unauthorised copying, use or disclosure.

7.3 Privacy

In performing its obligations under this agreement, the Licensee must comply, and use all reasonable efforts to ensure that its contractors comply, with all applicable legislation relating to privacy of personal information.

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Software Licence Terms

8 Exclusions and limitations

8.1 Acknowledgments

The Licensee acknowledges that:

(a) it has selected the Goods from a range of products and has satisfied itself that the Goods meet the Licensee's

requirements;

(b) no oral or written information, representation or advice given by or on behalf of Leica Microsystems, other than as

contained in this agreement, creates a warranty or in any way increases the scope of this agreement; and

(c) unless expressly agreed otherwise in writing, the Licensee has not relied on any information, representation or advice

given by or on behalf of Leica Microsystems in selecting the Goods; and

(d) Leica Microsystems makes no representation that the Goods conform to country, state or local laws, ordinances,

regulations, codes or standards (except as may otherwise be agreed to in writing by Leica Microsystems) and the Licensee is responsible for complying with all local laws relating to use of the Goods at its own cost.

8.2 Exclusion of implied terms

Leica Microsystems excludes from this agreement all conditions, warranties and liabilities implied or imposed by law or custom except any liability or implied condition or warranty the exclusion or limitation of which would contravene any statute or cause any part of this

8.3 Non-excludable conditions

To the extent permitted by law, Leica Microsystems’ liability for any breach of any Non-Excludable Condition is limited to:

(a) in the case of services, the resupply of the services or the cost of having the services supplied again (at Leica

Microsystems' option); and

clause 8 to be void (‘non-excludable conditions’).

(b) in the case of goods, the lowest of the cost of replacing the goods, acquiring equivalent goods or having the goods

repaired.

8.4 Exclusion of liability

To the extent permitted by law, Leica Microsystems excludes all liability (including liability for negligence) for:

(a) any indirect or consequential expenses, losses, damages or costs (including, without limitation, loss of profits, loss of

revenue, loss of or damage to data, failure to achieve anticipated savings or benefits, and any third party claims) incurred by or awarded against the Licensee under or in any way connected with this agreement or the use of the Software or Documentation;

(b) without limiting the foregoing, any expenses, losses, damages or costs incurred by or awarded against the Licensee

arising directly or indirectly in respect of clinical (including without limitation diagnostic, prescription and other treatment) errors made while using, or otherwise associated with the use of, the Software or Documentation; and

a result of its use of, any Third Party Material.

8.5 Limitation of liability

To the extent permitted by law, Leica Microsystems limits its total aggregate liability (including liability for negligence) for any damage arising under or in any way connected with this agreement or the use of the Software to Licensee for the Software or the Goods containing the Software under the Supply Agreement.

the price paid by the

9 Indemnity

The Licensee indemnifies Leica Microsystems against all expenses, losses, damages and costs (on a solicitor and own client basis) incurred by or awarded against Leica Microsystems arising directly or indirectly from or in relation to:

(a) any use of the Software not in compliance with this agreement;

(b) any breach of any Third Party Licence Terms by the Licensee;

(d) clinical (including without limitation diagnostic, prescription and other treatment) errors made while using, or

otherwise associated with the use, of the Software or Documentation;

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Software Licence Terms

(e) any failure by the Licensee to comply with laboratory practices that are consistent with industry practice, laws,

guidelines or decisions in the handling or use of the Software

(f) the Licensee's negligent acts or omissions; and/ortany other use or misuse of the Software by the Licensee.

10 Term and termination

10.1 Term

This agreement commences on the Effective Date and continues until terminated in accordance with this agreement.

10.2 Termination

(a) The Licensee may terminate this agreement at any time by destroying all copies of the Software and Documentation.

(b) The Licensee’s rights under this agreement will terminate immediately without notice from Leica Microsystems if the

Licensee fails to comply with any provision of this agreement or if the Licensee does not strictly observe the terms of payment under the Supply Agreement, and on termination, the Licensee must destroy all copies of Software and Documentation in its possession or control.

10.3 Accrued rights and remedies Termination of this agreement under this clause 10 does not affect any accrued rights or remedies of either party.

10.4 Survival Clauses 4 (Intellectual property), 7 (Confidentiality and privacy), 8 (Exclusions and limitations), 9 (Indemnity), 10.3

(Accrued rights and remedies), 10.4 (Survival), 11 (Force majeure) and 12 (General) continue after termination of this agreement.

11 Force majeure

Neither party will be liable for any delay or failure to perform its obligations pursuant to this agreement (other than on obligation to pay money) if that delay is due to Force Majeure. If a delay or failure of a party to perform its obligations is caused by or anticipated due to Force Majeure, the performance of that party’s obligations will be suspended. Either party may terminate this agreement if a Force Majeure persists for a continuous period of 90 days.

12 General

12.1 Severance

Part or all of any provision of this agreement that is illegal or unenforceable may be severed from this agreement and the remaining provisions will continue in force.

12.2 Entire agreement

This agreement (including any additional terms notified to the Licensee by Leica Microsystems) constitutes the entire agreement between the parties and supersedes any prior representations, warranties, understandings or agreements that relate to the same subject matter.

12.3 Variation

This agreement may only be amended by agreement in writing between the parties.

12.4 Governing law

This agreement is governed by the laws of the State of Victoria, Australia, and the parties submit to the non-exclusive jurisdiction of the courts in that State.

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Safety Notices

The Peloris™ tissue processor is designed to provide safe, trouble-free operation when used in accordance with this document. Follow all safety precautions to avoid personal injury, damage to patient samples, and damage to the instrument. Clean and maintain the instrument as described in

The Safety Notice Types section below describes the types of safety notices in the manual.

The General Warnings and Cautions section has general warnings for the Peloris instrument – other notices appear in relevant sections in the manual.

Safety Notice Types

Safety notices in this manual are either warnings or cautions.

Warnings

Warnings are notifications of hazards that could lead to personal injury to Peloris users or people in the vicinity of the instrument.

Warnings are also used when there is the possibility of damaging patient tissue samples.

Warnings in this manual use symbols with a red border, as illustrated below:

TOXIC HAZARD

There is danger of ingestion, inhalation or skin contact with toxic material.

Chapter 7, Cleaning and Maintenance.

HEAT HAZARD

There is danger of burns.

CHEMICAL HAZARD

There is a danger of exposure to corrosive chemicals.

ELECTRICAL HAZARD

There is danger of electric shock.

GENERAL HAZARD

There is danger of personal injury or damage to patient tissue samples.

Cautions

Cautions are notifications of hazards that could lead to damage to the Peloris instrument or other equipment.

Cautions in this manual use symbols with a yellow border, as illustrated below:

CAUTION

There is danger of damage to the Peloris instrument or other equipment.

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Safety Notices

General Warnings and Cautions

Persons operating the Peloris must be fully aware of the following warnings, in order to mitigate possible tissue damage or loss.

Reagent Configuration

WARNING

Always ensure that the reagents configured in the software are the actual reagents loaded on the instrument. A station containing different reagent could damage tissue samples.

Replacing Reagents

WARNING

Always change reagents when prompted. Always update station details correctly – never update the details without replacing the reagent. Failure to follow these directives can lead to tissue damage or loss.

WARNING

Do not alter the concentration of a used reagent unless you are able to verify the actual concentration. If the concentration is incorrect a reduction in tissue processing quality or damage to the tissue sample may result.

Protocol Validation

WARNING

Do not set new protocols as validated until they have passed the validation procedures for your laboratory. Only then should you edit the protocol to set it as valid, making it available to operators for clinical use (

4.1.4 Protocol Validation). Use of nonvalidated protocols may result in tissue damage or loss.

Basket and Cassette Loading

WARNING

Always ensure the cassettes are correctly inserted into the baskets and that the baskets are correctly placed in the retorts. Incorrectly placed cassettes or baskets may lead to samples being damaged as some tissue may not be fully covered by reagent during processing (see 2.2.4 Cassette Baskets).

WARNING

Never place three baskets into a retort when the instrument is configured with a two-basket fill level. If this occurs, reagent will not cover the top basket and tissue samples will be damaged.

Cleaning Protocol

WARNING

Remove all tissue from the retort before running a cleaning protocol as the dry step will damage the tissue.

see

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WARNING

Do not use cleaning protocols for reprocessing as the dry step will damage the tissue.

WARNING

Do not load unprocessed tissue samples into a retort prior to running a cleaning protocol. Formalin in the residue purged to the wax bath at the start of the cleaning run may damage tissue on subsequent runs.

If you inadvertently load unprocessed samples into a retort prior to running a cleaning protocol, remove the samples and attempt to load a processing protocol before loading the cleaning protocol. The purge before the cleaning run will be skipped.

Instrument Setup

WARNING

Do not use the instrument without installing the drip tray.

WARNING

The instrument must be installed and configured by an approved service representative.

Safety Notices

WARNING

Always use suitably rated lifting equipment (such as a trolley or forklift) when moving a Peloris tissue processor more than a few metres.

Only use the instrument’s castors to reposition an instrument for service access.

Electrical Hazards

WARNING

The Peloris tissue processor must be connected to an earthed mains power outlet socket.

WARNING

Dangerous voltages are present inside the Peloris tissue processor. Only service technicians approved by the Biosystems Division of Leica Microsystems should remove any of the instrument’s covers or access the internal components.

WARNING

The instrument’s operating voltage is factory set and it must not be changed. Severe damage will occur if an instrument is connected to an incorrect power supply voltage.

WARNING

Do not pull out the mains cable whilst the instrument is operating unless there is an emergency situation and both the front panel power button and the mains wall switch are inaccessible.

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Reagents

Safety Notices

WARNING

Locate the instrument so that either the mains wall outlet or the instrument’s appliance inlet socket is accessible. You must be able to disconnect the mains power cable without moving the instrument.

WARNING

Do not move the instrument unless the power cable is disconnected.

WARNING

Chloroform vapors may cause severe injury, incapacitation, or death. When using chloroform with the Peloris tissue processor, Leica Microsystems recommends that an external

fume extraction system be installed. Chloroform vapors may accumulate during normal operation or in the unlikely event of a spill. The extraction system must keep these vapors below dangerous levels.

Never open a retort that contains chloroform or chloroform residue.

WARNING

Do not heat reagents above their boiling points. Boiling reagents will release large quantities of fumes that may overload the internal carbon filter or (if fitted) the external filtering system. Boiling reagents are also likely to lead to excessive pressures within the instrument, increased reagent contamination and reagent spills.

Reagent boiling points are lower when in a retort operating with a vacuum or with pressure/vacuum cycling.

WARNING

Handle and dispose of reagents and condensate in accordance with all relevant procedures and government regulations that apply at the laboratory site.

WARNING

Do not use fixatives containing picric acid as picric acid is explosive when dry.

WARNING

Molten wax is hot and may cause burns. Use caution when handling wax and removing baskets.

CAUTION

Do not use acetone or other ketones. These damage the instrument’s valves.

CAUTION

Do not use reagents containing corrosive chemicals such as mercuric salts, picric acid, nitric acid and hydrochloric acid.

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Regulatory Approvals

IEC 61010-1  2nd Edition

UL 61010A-1 Safety requirements for electrical equipment for measurement, control and laboratory use – Part 1

CAN/CSA C22.2 No.1010-1

IEC 61010-2-010 Safety requirements for electrical equipment for measurement, control and laboratory use – Part 2

IEC 61010-2-081 Safety requirements for electrical equipment for measurement, control and laboratory use – Part 2

IEC 61326 Electrical equipment for measurement, control and laboratory use – EMC requirements FCC Part 15 Class A/B Unintentional Radiators ISO 13485: 2003 Medical Devices – Quality management systems – Requirements for regulatory compliance

Safety requirements for electrical equipment for measurement, control and laboratory use – Part 1 General requirements

General requirements

Safety requirements for electrical equipment for measurement, control and laboratory use – Part 1 General requirements

Particular requirements for the heating of materials

Particular requirements for automatic and semi-automatic laboratory equipment for analysis and other purposes

FCC Compliance

This device complies with part 15 of the FCC Rules. Operation is subject to the following two conditions:

1. This device may not cause harmful interference

2. This device must accept any interference received, including interference that may cause undesired operation.

FCC Class B compliance statement

This equipment has been tested and found to comply with the limits for a Class B digital device pursuant to part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference in a residential installation. This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance with the instructions, may cause harmful interference to radio communications. However, there is no guarantee that interference will not occur in a particular installation. If this equipment does cause harmful interference to radio or television reception, which can be determined by turning the equipment off and on, the user is encouraged to try to correct the interference by one or more of the following measures:

 Reorient or relocate the receiving antenna

 Increase the separation between the equipment and receiver

 Connect the equipment into an outlet on a circuit different from that to which the receiver is connected

 Consult the dealer or an experienced radio or television technician for help.

CE Marking and European Union Notice

The CE mark on the equipment indicates compliance with the EEC Directives for Electromagnetic Compatibility (89/336/EEC), Waste Electrical and Electronic Equipment (02/96/EC), Restriction on the Use of Certain Hazardous Substances in Electrical and Electronic Equipment (02/95/EC), and In Vitro Diagnostic Medical Devices (98/79/EC). Marking of equipment in this manner denotes that the equipment meets the technical standards detailed above.

Declaration of Conformity

A “Declaration of Conformity” in accordance with the preceding directives and standards has been made, and is on file at Leica Biosystems Newcastle Ltd, Balliol Business Park West, Benton Lane, Newcastle upon Tyne, NE12 8EW, United Kingdom.

Note: To maintain compliance with the above CE and FCC Rules and Regulations, use only the cables supplied with the equipment.

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Legal Notices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2

Contacting Leica Microsystems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Software Licence Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Safety Notices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Regulatory Approvals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

1 Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17

1.1 Summary of Chapters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .18

1.2 Using the Software. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

Basic Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Navigation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Access Levels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

1.3 Help . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

2 Hardware. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .23

2.1 Switching On and Shutting Down. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

2.2 Retorts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Opening and Closing Retort Lids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Fill Levels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26

Magnetic Stirrer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

Cassette Baskets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28

2.3 Wax Bath . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

2.4 Reagent Cabinet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

Reagent Bottles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Condensate Bottle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .34

Carbon Filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

2.5 Touch-screen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

2.6 External Vapor Removal Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

2.7 Alarm Connections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

3 Running Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .40

3.1 Quick Start – Running a Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

3.2 Cleaning Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

3.3 Status Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

Status Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46

Protocol Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

3.4 Protocol Run Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Scheduling Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .50

Editing the Protocol for a Single Run . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53

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3.5 Pausing and Abandoning Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54

3.6 Retort Scheduling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Delayed End Times and Initial Fills. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Unavoidable Reagent Clashes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

Unavailable Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57

4 Protocol Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .58

4.1 Protocol Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Protocol Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59

Reagent Selection Method. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60

Pre-defined Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .61

Protocol Validation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Carryover Setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62

Saving Protocol Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

4.2 Creating, Editing and Viewing Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

The Protocol Selection Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Editing Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66

Creating New Protocols. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70

Viewing Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71

5 Reagent Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .72

5.1 Reagents Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72

Reagent Groups, Types and Stations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Concentration Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

Thresholds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76

Recommended Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78

Tissue Marking. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Reagent Compatibility. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .80

5.2 Managing Reagent Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Pre-defined Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80

Editing Active Reagent Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Managing the Reagent Types Lists . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83

5.3 Managing Reagent Stations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Reagent Stations Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84

Setting Reagent Station Properties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

5.4 Replacing Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Remote Fill/Drain Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88

Remote Fill/Drain Connections. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Replacing Reagent – Remote Fill and Drain. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Replacing Reagent – Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94

Replacing Wax . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Filling and Draining Retorts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97

6 Settings & Ancillary Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .98

6.1 Reagents Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98

Manual Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .99

Reagent Management. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101

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6.2 Control Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Instrument Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103

Device Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105

Service Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Event Log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106

Alarms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107

Access Level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108

File Transfer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109

7 Cleaning and Maintenance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .114

7.1 Cleaning and Maintenance Schedule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

7.2 Daily Tasks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

7.3 Weekly Tasks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

7.4 60–90 Days . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122

7.5 Retort Acid Clean . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123

8 Reference . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .124

8.1 Reagent Threshold Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

8.2 Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

Specimen Type and Protocol Duration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

List of Pre-defined Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126

Xylene Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127

Xylene-free Protocols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131

Cleaning Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134

8.3 Station Configurations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135

8.4 Protocol Step Temperatures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

8.5 Reagent Compatibility Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

9 Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .139

9.1 Preliminary Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

9.2 Flowcharts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140

Under-processed Tissue – Instrument Setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141

Over-processed Tissue – Instrument Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

Under- or Over-processed Tissue – Reagents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Poor Processing – Incorrect Protocol . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144

Poor Processing – Correct Protocol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145

Cutting Artifact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146

Staining Artifact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147

Block Artifact . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148

9.3 Reprocessing Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149

10 Consumables and Accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .153

11 Specifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .154

Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .156

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Introduction

The Leica Peloris™ rapid tissue processor is a dual retort tissue processor that offers fast, high quality tissue processing for histology laboratories. With reagent capacity sufficient to run the two retorts independently, it allows a high degree of scheduling flexibility. Intelligent software lets you configure the instrument to suit your laboratory’s workflows while providing checks and restrictions that help you avoid mistakes that could damage tissue. The reagent management system closely tracks reagent condition. Depending on your setup, it uses this information to select the optimal reagent for each protocol step. It alerts you when to replace reagent so that quality is never compromised, at the same time ensuring you get full use of all reagents. The clear, intuitive, touch-screen interface makes loading and monitoring runs easy, and protocol configuration, reagent setup and other system settings are equally straightforward. And behind all this you have the support of Leica Microsystems, with years of experience developing top quality, industry-leading histology equipment.

Congratulations on your purchase of the Leica Peloris rapid tissue processor. We trust it will provide you with years of fast, efficient, high quality tissue processing.

This chapter has the following sections:

 1.1 Summary of Chapters

 1.2 Using the Software

 1.3 Help

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1.1 Summary of Chapters

 Chapter 1, Introduction: general introduction, chapter summary, general instructions for

using the software, and help resources.

 Chapter 2, Hardware: descriptions of the main components of the Peloris instrument.  Chapter 3, Running Protocols: main steps for running protocols, further configuration

options and scheduling, monitoring processing on the Status screen.

 Chapter 4, Protocol Setup: descriptions of protocol types and the reagent selection

methods used; protocol validation and the carryover setting. Creating and editing protocols.

 Chapter 5, Reagent Setup: reagent groups, types and stations, and reagent management

on the Peloris. Setting up reagent types and stations in the software. Replacing reagents.

 Chapter 6, Settings & Ancillary Operations: basic instrument settings, independent

operation of instrument components, event monitoring, alarms, and transfer of system files.

 Chapter 7, Cleaning and Maintenance: daily and as-required maintenance, accessories

available from Leica Microsystems.

 Chapter 8, Reference: descriptions of the pre-defined protocols and recommended bottle

configurations. Recommended reagent thresholds and reagent compatibility tables.

Introduction

 Chapter 10, Consumables and Accessories: a list of Peloris consumables and accessories

with part numbers for easy ordering.

 Chapter 11, Specifications: system specifications.

1.2 Using the Software

Control all instrument functions from the touch-screen. This section describes basic touch-screen operation and how to navigate the software, with a summary of all the software screens. It also describes user access levels.

See sections:

 1.2.1 Basic Operation

 1.2.2 Navigation

 1.2.3 Access Levels

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1.2.1 Basic Operation

Buttons

Tap buttons to open menus, screens and dialogs, and to start and stop actions in the instrument. Enabled buttons are blue and appear raised. Selected buttons are orange and appear sunken. Disabled buttons are dimmed.

Figure 1. Button states—selected, available and unavailable

Icons

Icons are used to represent various Peloris tissue processor elements including reagent stations and retorts. Selectable icons appear raised. A selected icon appears raised with a red outline. Nonselectable elements appear flat and are used for indication only. Select an icon by tapping it, as you would a button.

Introduction

Figure 2. Reagent station—selectable, selected, not selectable

Tables

Tables display configuration information such as reagent station and protocol setup. You can edit some table cells but others are locked. The background color of locked cells is dimmed. Select editable table cells by tapping within the cell boundaries.

Figure 3. Table cells—editable (1) and locked (2)

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Introduction

Keypads

Keypads appear as needed to allow you to enter text and numbers. There are two types of keypad: alphanumeric (text and numbers) and numeric (numbers only). The keypads are analogous to a computer keyboard with on-screen buttons acting as keys (1). Enter text and numbers by tapping

the appropriate buttons in order and use the Caps Lock button (4) or Shift button (5) to select

upper or lower case characters. As you type, the characters you select are displayed in the text

window (6). The alphanumeric keypad has a Back Space button (7) to delete the last character while all keypads include a Clear button (3) to remove all characters. When you have finished, tap the Esc button (2) to exit without saving or the Enter button (8) to confirm your entry.

1.2.2 Navigation

Navigate the software from the Function bar at the top of the screen.

The Function bar is always visible, so you can always find the screen you want. Tap a button in the bar to change screens immediately or open a menu with buttons for a number of related screens.

Some screens have alternative “views” to divide the information presented. For example, the

Reagent stations screen has two views, one each for bottle and wax chamber information. Use

buttons on the screens themselves to move between the alternative views.

Figure 4. Alphanumeric keypad

Figure 5. The Function bar

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Introduction

The table below lists all the screens in the Peloris software with brief descriptions of the screen functions, and links to relevant sections of the manual.

Function bar button

Menu button Screen purpose Refer to:

Status —

Protocols —

Stations

Types

Reagents

Remote fill/ drain

Manual operations

Management

Instrument settings

Device settings

Load and run protocols, and view system

3.3 Status Screen

status.

Select, create, edit and manage protocols. 4.2 Creating, Editing

and Viewing Protocols

Set up reagent stations. You can also view the current reagent concentrations and wax

5.3 Managing Reagent Stations

bath temperatures.

Manage your list of active reagent types. 5.2 Managing Reagent

Typ e s

Fill or drain reagent bottles and drain wax

5.4 Replacing Reagents

stations.

Manually control individual instrument components.

6.1.1 Manual Operations

Set basic reagent management options. 6.1.2 Reagent Manage-

ment

Set options for time display, the carbon filter, fill levels and manual operation drip

6.2.1 Instrument Settings

time.

Change sound, touch-screen and alarm set-

6.2.2 Device Settings

tings.

Service

Control

settings Event log Alarms Access level File transfer

Help —

View the instrument serial number and soft-

6.2.3 Service Settings

ware versions.

View all system events. 6.2.4 Event Log

Clear or silence active alarms. 6.2.5 Alarms

Set the access level. 6.2.6 Access Level

Transfer files to and from the instrument. 6.2.7 File Transfer

Open an HTML version of the user manual

1.3 Help

in the Peloris software.

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1.2.3 Access Levels

Peloris has two user access levels available to laboratory staff: operator and supervisor. Operators can carry out all routine tasks such as running protocols and replacing reagents. But operators cannot edit protocols or set bottle configurations – you must have supervisor rights for these actions. Supervisors also have greater rights to configure the system.

Some configuration settings displayed in the software require service level access to change. These are provided so you can view the settings, but you must contact your customer support representative if you want to change them.

You automatically begin at operator level when you start the software. Supervisors need a

password to change to their access level on the access level screen (Control menu, Access level).

If a supervisor does not interact with the software for more than 10 minutes the access level automatically reverts to operator.

An icon on the Function bar indicates your current access level.

Introduction

1.3 Help

This user manual is provided in PDF format on a CD. It is also included (in HTML format) in the

Peloris software. Tap the Help button in the Function bar to open. Use buttons on the Help screen

and links in the text to navigate the online Help.

Figure 6. Access level icons with operator (1) and supervisor (2)

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Two r e tor t s

Reagent cabinet

Wax bath:

with four wax chambers

Touch-screen

Power button

Hardware

The Peloris™ tissue processor is a free-standing processor with two retorts, sixteen reagent bottles and four wax chambers. A touch-screen mounted on the top of the instrument connects to an on-board computer for control of all instrument operations.

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Figure 1. Peloris tissue processor – main features

Page 24

This chapter describes the main features of Peloris instrument.

See sections:

 2.1 Switching On and Shutting Down

 2.2 Retorts

 2.3 Wax Bath

 2.4 Reagent Cabinet

 2.5 Touch-screen

 2.6 External Vapor Removal Systems

 2.7 Alarm Connections

2.1 Switching On and Shutting Down

Under normal conditions keep the Peloris on at all times, even when idle for extended periods. Shut down for servicing or if moving the instrument.

Hardware

Start

1. Plug the power cable into the mains socket and switch on the power.

2. Press the power button to start the instrument.

Normal Shutdown

For a normal shutdown the instrument must be idle with no protocols or other operations in progress:

1. Tap the shutdown button on the Function bar to shut down the software in an orderly manner.

2. Wait for the touch-screen to go blank then press the power button to remove all power from the instrument.

3. Switch the power off at the mains socket and pull out the power cable.

Emergency Shutdown

For emergency shutdown, press the power button immediately.

If conditions permit, switch the power off at the mains socket and pull out the power cable.

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2.2 Retorts

The Peloris tissue processor has two independent processing retorts with each retort holding up to 300 tissue samples in three Peloris cassette baskets. Each retort operates independently with separate temperature, pressure/vacuum and stirrer speed control. The Peloris tissue processor schedules resources to ensure both retorts operate efficiently with one set of reagents.

 2.2.1 Opening and Closing Retort Lids

 2.2.2 Fill Levels

 2.2.3 Magnetic Stirrer

 2.2.4 Cassette Baskets

2.2.1 Opening and Closing Retort Lids

Use the handles on the front of the instrument to latch and unlatch the retort lids.

Hardware

Figure 2. Opening a retort lid

Always be aware of the contents, temperature and pressure of a retort before opening it. In some cases you may need to set the retort pressure and temperature manually before you can safely open it (see

You may see a warning if the retort temperature is greater than either the retort empty access

temperature (view on the Reagent management screen) or the safe access temperature associated with the reagent in the retort (set on the Reagent types screen).

The retort lids can be removed for cleaning (see Clean Lids and Seals in 7.2 Daily Tasks).

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Venting a Retort below).

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Hardware

Some instruments have retort latch locks to disallow opening retorts when a protocol is running or the retort temperature is high. See your service representative if you have latch locks on your instrument.

WARNING

Retorts may contain very hot fluid that could cause severe burns. Wear suitable protective clothing and eyewear when opening a retort.

WARNING

Retorts may contain hazardous reagents and vapors. Wear suitable protective clothing and eyewear and ensure adequate ventilation when opening a retort.

WARNING

Take care not to knock retort lids when they are open. They could crush fingers or hands.

Venting a Retort

You must ensure there is no pressure or vacuum inside a retort before you open the lid. The retorts automatically vent at the start and end of a protocol, and also during a pause in a protocol. However, you may need to manually vent a retort if an automatic vent fails or if you wish to access a pressurized or evacuated retort at other times.

Use the Manual operations screen to manually vent the retorts. Set the Pressure button to Ambient for the retort that you want to open. You may need to wait up to one and a half minutes for the pressure to equalize. If your instrument has retort latch locks, use the Lock/Unlock retort

button; it may take several cycles to successfully vent a retort.

If you leave a hot retort closed for an extended time, the air in the retort will cool and create a vacuum. You must then vent the retort before attempting to open the lid.

2.2.2 Fill Levels

Retorts can be filled with enough reagent for two or three cassette baskets. Supervisors set the

required fill level on the Instrument settings screen (see

Settings).

The two basket fill volume is 3.8 liters (1 gallon US) and the three basket fill volume is 5 liters (1.32 gallon US).

Use markings on the reagent bottles (Figure 3) and wax chambers (Figure 4) to ensure you have enough reagent to fill the retorts to the required level. Always keep the reagent or wax volumes

Reagent Fill Levels in 6.2.1 Instrument

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Hardware

well above the markings, but below the maximum (MAX) level. Reagent levels below the minimum will cause protocols to either fail or use a sub-optimal reagent sequence.

Figure 3. Bottle fill levels Figure 4. Wax chamber fill levels

Liquid Level Sensors

Figure 5. Liquid level sensors for—

maximum (1), three-basket (3) and two-basket (2) retort fill levels

Each retort has three liquid level sensors to monitor fluid levels. The two lower sensors monitor the two and three basket levels. The top, maximum, sensor responds to a fluid level of 5.3 liters. It serves a safety function ensuring no more reagent is pumped into the retort if triggered.

The sensors may occasionally be affected by a buildup of condensation or deposited material. If this occurs the software will direct you to wipe the appropriate sensor. Always ensure the sensors are kept clean as part of regular retort cleaning (see

Clean Retorts in 7.2 Daily Tasks).

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2.2.3 Magnetic Stirrer

Each retort has as magnetic stirrer that stirs the reagent or wax to ensure temperature consistency and good tissue penetration. The stirrer is driven by a magnetically-coupled external motor. The stirrer speed can be controlled for each protocol step and is easily removed for cleaning (see Retorts in 7.2 Daily Tasks).

Hardware

Clean

Figure 6. Magnetic stirrer (1)

2.2.4 Cassette Baskets

There are two Peloris basket types: the configurable high-capacity basket that accommodates the maximum number and type of cassettes; and the spaced basket that ensures optimal reagent flow.

The high-capacity cassette baskets accept most common cassette types and include configurable dividers that allow for different cassette sizes and packing densities.

The spaced baskets include dividers that ensure optimum reagent flow with minimal carryover. This basket type accepts 72 standard cassettes. Spaced baskets must be used for all xylene-free protocols.

Cassette baskets stack into the retorts with the lids upwards and handles dropped flat. Make sure the first basket sits flat on the rack on the pins at the bottom of the retort ( additional baskets so they sit flat on the lower ones – crooked baskets can leave cassettes exposed, damaging the tissue in them.

Figure 8). Stack

Figure 7. Placing a basket into a retort Figure 8. Retort pins

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WARNING

Never place three baskets into a retort when the instrument is configured with a two-basket fill level. If this occurs, reagent will not cover the top basket and tissue samples will be damaged.

Opening and Closing Cassette Baskets

The lid is held by two catches and is completely removable to aid cassette access.

Hardware

Figure 9. Releasing the lid Figure 10. Replacing the lid

 To remove the lid, release one catch then swing the lid up and off the basket (see Figure 9).

 To replace the lid, insert one end into a catch then swing the other end down so it firmly

engages the second catch (see

 Make sure the lid is firmly held by both catches or the body and cassettes may fall when the

Figure 10).

basket is lifted.

High-capacity Baskets

High-capacity baskets include dividers to configure the baskets to hold different numbers of cassettes. Use all the dividers to configure the baskets for orderly packing (up to 88 cassettes) or the long dividers only for tight packing (up to 100 cassettes).

For orderly packing, insert both the long and short dividers into the basket. This arrangement makes it easier to insert and remove the cassettes (see

Figure 11 and Figure 12). Six standard

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Hardware

cassettes can be placed in the end sections of each row and five in the middle sections, giving 88 cassettes per basket.

Figure 11. Basket arranged for orderly packing Figure 12. Basket packed with 88 cassettes

For tight packing, insert only the long dividers. This allows you to pack the maximum number of cassettes — 25 per row (see

Figure 13 and Figure 14).

Figure 13. Basket arranged for tight packing Figure 14. Basket packed with 100 cassettes

For large or unusually shaped cassettes use the baskets with all dividers removed.

CAUTION

Do not use high-capacity baskets for xylene-free protocols as this may lead to wax build up that will eventually require service intervention.

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Hardware

Spaced Baskets

The spaced baskets include a fixed divider that ensures that the cassettes are correctly spaced for optimal processing. Each spaced basket can fit up to 72 standard cassettes inserted into the spacing springs as shown in

You must use spaced baskets when running xylene-free protocols.

Figure 15.

Figure 15. Detail of cassettes packed into a spaced basket

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2.3 Wax Bath

The wax bath at the top rear of the instrument has four wax chambers accessed by two lids. Each chamber acts independently, holding enough wax to fill a retort. Although wax does not move between the chambers, they are connected for air flow and so always have the same pressure.

Use the lid handles to open the lids. Always use the handles to close the lids, ensuring the lids are properly latched. Be sure not to knock the lids when they are open as they may slam shut.

Always ensure the wax bath pressure is at ambient pressure before opening the lids. If the pressure is not ambient, vent the bath first. You can do this when you pause a running protocol or from the

Manual operations screen.

Hardware

Figure 16. Opening a wax bath lid

View the current temperature of each wax station in the wax chambers view of the Reagent stations screen.

Depending on the reagents you use you can set the instrument to clean the wax in the bath (see Wax Bath Settings in 6.1.2 Reagent Management).

Drain used wax with commands on the Remote fill/drain screen. Directly fill with molten or solid

wax (see

5.4.5 Replacing Wax).

WARNING

Take care when opening the wax bath after a xylene-free protocol as the protocol will leave very hot wax in the bath.

WARNING

Never open a wax bath lid when there is wax in a retort or wax is being transferred; hot wax may splash out of the bath.

WARNING

Take care not to knock wax bath lids when they are open. They could crush fingers or hands.

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2.4 Reagent Cabinet

16 reagent bottles

Carbon filter

Condensate bottle

Hardware

Figure 17. Reagent cabinet

The reagent cabinet houses the reagent bottles, carbon filter, and condensate bottle. The cabinet has two glass doors that retract into the cabinet when open.

WARNING

To reduce the risk of fluid spills, always keep the reagent cabinet doors closed during instrument operation unless actually changing a reagent or emptying the condensate bottle.

 2.4.1 Reagent Bottles

 2.4.2 Condensate Bottle

 2.4.3 Carbon Filter

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2.4.1 Reagent Bottles

The reagent cabinet holds sixteen reagent bottles. This is three more than standard tissue processors and it ensures there are sufficient reagents to simultaneously schedule protocols in both retorts while also having ample cleaning reagents on board and ready to use. The bottle at each station holds sufficient reagent to fill a single retort.

To remove a bottle, lift open the cabinet door and pull the bottle out. Push back in position to return – you will feel the bottle pushing into its connection point on the back of the cabinet. Replace reagent in the bottles either manually, with the bottles removed from the instrument, or in

position on the instrument using the Remote fill/drain screen (see

Screen).

Some chemicals may cause the bottles to expand over time; this is normal and does not impact the performance of the instrument.

WARNING

Never run the instrument with missing bottles or with loose or missing bottle lids as fluid spills and vapor leaks will occur.

Hardware

5.4.1 Remote Fill/Drain

2.4.2 Condensate Bottle

A separate bottle collects condensate fluid. It sits beside the reagent bottles in the lower section of reagent cabinet. Empty weekly. Do not allow the bottle to overflow as condensate fluid will spill from the instrument or contaminate other reagents.

WARNING

Never run the instrument with the condensate bottle missing or its lid either loose or missing as fluid spills and vapor leaks will occur.

2.4.3 Carbon Filter

The carbon filter absorbs reagent fumes to prevent them from entering the laboratory atmosphere.

To ensure the filter is operating effectively, it must be replaced periodically. Use the Carbon filter threshold button to set the replacement interval (see

The carbon filter can be bypassed and the instrument connected to an external vapor removal system (see 2.6 External Vapor Removal Systems).

WARNING

Never run the instrument without the carbon filter or an external filter system; this will release potentially dangerous fumes into the laboratory.

6.2.1 Instrument Settings).

The filter must be installed with the direction arrow on the front pointing up and the locking mechanism closed (see

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Change Carbon Filter in 7.4 60–90 Days).

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2.5 Touch-screen

A touch-screen mounted on the right of the Peloris connects to a computer in the instrument that controls all instrument operations.

Use the Peloris software on the touch-screen to configure the instrument, run protocols, and perform ancillary operations such as replacing reagents. Tap buttons and icons with your finger or a blunt object – do not use sharp objects. Ensure no strong solvents come into contact with the touch-screen.

Optional stick-on/ peel-off touch-screen protectors, provided by Leica Microsystems, can be used to protect to the touch-screen.

In its normal operating position the touch-screen sits over the wax bath lid, but can be rotated to give clearance to open the lid. The screen can be remounted so its normal position is to the right of the mounting stem rather than over the instrument. See your service representative if you want to change the touch-screen position.

CAUTION

If the touch-screen goes blank or is unreadable, turn off the instrument immediately.

Hardware

2.6 External Vapor Removal Systems

Figure 18. Vapor select valve (1) and vapor outlet (2)

The outlet for instrument vapors can be switched between the internal carbon filter and an external vapor extraction system. At the rear of each instrument there is a valve that directs vapors to either the carbon filter or to an outlet that can be connected into the external system.

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Hardware

 For instructions on changing to an external vapor system, see Connecting to an External

System below.

 For instructions on returning to the internal carbon filter system, see Returning to the Internal

Filter System.

Some instruments do not have the vapor select valve fitted. However your service representative can easily connect these instruments to an external vapor system.

Connecting to an External System

WARNING

When the vapor select valve is in the external position, you must ensure an external vapor system is correctly installed or potentially dangerous fumes will be released into the laboratory environment.

Use the following procedure to connect the instrument to an external vapor system.

1. Connect the instrument’s vapor outlet into the external system (see item 2 in Figure 18).

2. Turn the vapor select valve a quarter turn anticlockwise to direct vapors to the vapor outlet (see

Figure 19).

Note: to access the valve you may need to remove a blanking plug.

Figure 19. Vapor select valve in the external system position

3. Set the carbon filter threshold to one of the following options.

(i) The inspection interval for the external system (see 6.2.1 Instrument Settings).

(ii) The maximum value (1000) to limit the number of unwanted warnings (see 6.2.1

Instrument Settings).

(iii) Overridden (contact your service representative to arrange this setting).

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Hardware

Returning to the Internal Filter System

WARNING

When the vapor select valve is in the internal position, you must ensure the carbon filter is correctly installed or potentially dangerous fumes will be released into the laboratory environment.

Use the following procedure to reconfigure an externally connected instrument to internal carbon filter use.

1. Ensure a new carbon filter is correctly installed (see 2.4.3 Carbon Filter).

2. Turn the vapor select valve a quarter turn clockwise to direct the vapors to the internal carbon filter (see

Note: to access the valve you may need to remove a blanking plug.

Figure 20).

Figure 20. Vapor select valve in the internal filter position

3. If required, disconnect the external system from the vapor outlet (see item 2 in Figure 18). You may leave the external system connected as the vapor valve effectively isolates this outlet.

4. Set the carbon filter threshold to a value appropriate for your instrument’s work load.

We recommend an initial threshold of 60 days with adjustments only if you are sure the carbon filter is becoming saturated earlier or is still in good condition after this time (see

6.2.1

Instrument Settings).

If the carbon filter threshold has been overridden the carbon filter buttons will not be available. Arrange for your service representative to cancel the override.

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2.7 Alarm Connections

Figure 21. Remote alarm (1) and local alarm (2) connectors

Each Peloris tissue processor has two external alarm connections — a local alarm connection and a remote alarm connection (see alarm indication devices including audible alarms, visual alarms or automatic phone dialers.

Speak to your service representative to configure the events that will trigger each of the external alarms, and to set whether the alarms are a single signal or continuous.

Figure 21). These connections may be used to control a range of

Hardware

Alarm Connector Specifications

The load connected to either alarm connector must not exceed the following specifications.

 Maximum voltage: 

30 V DC

 Maximum current: 

1 A (resistive load)

 Maximum current: 

0.5 A (inductive load)

Alarm Connector Pins

Each alarm connector has three pins as follows (see Figure 22):

 Pin 1 — Normally open (item 1)

 Pin 2 — Normally closed (item 2)

 Pin 3 — Common (item 3)

Figure 22. Alarm connector pins

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Hardware

Pin Schematic During Normal Operation

When the instrument is operating normally (no alarm) the alarm pins connect as shown in Figure

23.

 Pin 1 (normally open) is open.

 Pin 2 (normally closed) is connected to

Pin 3 (common).

Figure 23. Alarm pins in normal state

Pin Schematic During Alarm Conditions

When the instrument has an active alarm, the alarm pins connect as shown in Figure 24 below.

 Pin 1 (normally open) is connected to

Pin 3 (common).

 Pin 2 (normally closed) is open.

Figure 24. Alarm pins in alarm state

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Running Protocols

This chapter describes how to run protocols on the Peloris™ system. The first section gives all the steps to run a protocol once reagents and protocols have been configured. The second describes cleaning protocols, and the

third describes the Status screen, where you control and monitor processing. The fourth and fifth sections give

details about modifying or pausing protocol runs. The sixth section discusses general issues about scheduling protocols.

 3.1 Quick Start – Running a Protocol

 3.2 Cleaning Protocols

 3.3 Status Screen

 3.4 Protocol Run Options

 3.5 Pausing and Abandoning Protocols

 3.6 Retort Scheduling

3.1 Quick Start – Running a Protocol

Follow the instructions below to run a protocol.

Before you begin all the reagents you need must be configured and there must be a validated protocol ready to load. See Protocols for direction on these topics.

Instrument Checks and Setup

1. On the screen, tap the Status button to view the Status screen:

(i) Check that the retort icon shows the retort is clean or has residue of a reagent compatible

with the first reagent of the protocol.

(ii) Check for hatched bottle or wax chamber icons.

Replace the reagent in hatched stations (see 5.4 Replacing Reagents).

5.3 Managing Reagent Stations and 4.2 Creating, Editing and Viewing

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Running Protocols

2. Check that the instrument is ready:

(i) All 16 bottles are properly installed on the instrument.

(ii) There is enough reagent in the bottles and wax chambers.

Fill to at least the MIN 2 level if you fill retorts to the two-basket level, or at least the MIN

3 level for the three-basket level (view the instrument fill level in the Reagent fill

levels section on the Instrument settings screen).

(iii) Open the retort to use. Check that it is clean, or that any residue is a reagent compatible

with the first reagent in the protocol.

3. Prepare your cassettes and load them into baskets (see 2.2.4 Cassette Baskets).

Load Protocol

4. Tap the Select button at the bottom left or right corner of the Status screen, depending on

the retort you want to use.

The Protocol selection screen opens.

5. Select a protocol and tap Load.

Only validated protocols can be selected by operator-level users (see 4.1.4 Protocol Validation).

The Status screen reopens with the protocol loaded.

Run Protocol

6. Tap the Run button.

Review any warnings and rectify as required. If necessary, cancel the warnings dialog box while you rectify conditions.

If the first step of the protocol uses a reagent that is incompatible with retort residue you may need to abandon the protocol to run a cleaning protocol. Alternatively, you may be able to skip the first steps of the protocol (see

Continue in the warnings dialog box.

7. If prompted, enter the number of cassettes in the run in the Number of cassettes dialog

box.

It is important to enter the correct number of cassettes – this is used by the reagent management system to calculate reagent concentrations.

8. Open the retort lid and insert the cassettes when directed in the Insert cassettes dialog box. Tap Done in the dialog box when you have inserted the cassettes and closed the retort.

9. View the protocol end-time in the Scheduling dialog box. If acceptable, tap Start, or set a different end time (see 3.4.1 Scheduling Protocols). Tap Edit steps in the Scheduling dialog box to skip initial protocol steps or change step

durations (see

3.4.2 Editing the Protocol for a Single Run).

10. When you tap Start the system schedules the protocol.

 If the system is unable to schedule the protocol, you will see a list of errors. Tap OK and

correct all errors before attempting to run the protocol again (see Reagent Clashes for a description of possible scheduling difficulties).

 If the system was able to schedule the run, the protocol will begin.

 If you have set a delayed end time, an initial fill condition will occur (see 3.6.1 Delayed

End Times and Initial Fills).

3.4.2 Editing the Protocol for a Single Run). If so, tap

3.6.2 Unavoidable

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Running Protocols

11. View the progress of the protocol in the Status screen.

You can pause processing to add additional cassettes, or abandon protocols completely (see

3.5 Pausing and Abandoning Protocols).

Finish Protocol Run

12. When the protocol is finished the Protocol complete dialog box opens and the alarm sounds; tap OK to continue.

13. Tap Drain retort before accessing from the Drain/Access retort dialog box. You can remove the baskets before draining the retort (tap Access retort now) – this option

is not recommended.

14. Wait for the Retort accessible dialog box to appear then open the retort and remove the

cassettes.

Tap OK to close the dialog box.

Run Cleaning Protocol

15. The Run cleaning protocol dialog box appears. (i) Recommended: tap Clean now to load a cleaning protocol.

If you have more than one cleaning protocol use the Prev and Next buttons to select the

protocol you want to use.

(ii) Not recommended: tap Clean later to end the procedure and leave the retort full or with

residue in it.

If you select this option heating continues to keep the wax in the retort and valves molten.

See 3.2 Cleaning Protocols below for information about cleaning protocols.

16. Place the used cassette baskets into the retort when prompted with the Insert baskets dialog

box.

Remove all tissue as the cleaning protocol will damage any tissue left in the retort.

Tap Done in the dialog box when you have inserted the baskets and closed the retort.

17. Tap Start in the Scheduling dialog box to begin the run.

If required change the protocol’s end time before starting.

18. View the progress of the protocol in the Status screen.

19. When the protocol is finished the Protocol complete dialog box opens and the alarm sounds; tap OK to continue.

20. When the Remove baskets dialog box appears, open the retort lid and remove the baskets. Tap OK to continue.

21. Tap Unload protocol in the Status screen so the retort is available for the next protocol.

WARNING

Do not open a retort while a protocol is running as the retort could be pressurized and may contain hot reagent and fumes. Always follow the retort access instructions detailed in 3.5 Pausing and Abandoning Protocols if you need to access a retort during processing.

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3.2 Cleaning Protocols

Cleaning protocols clean the retorts and reagent lines. Always run a cleaning protocol as soon as

possible after processing runs; unless there are specific reasons not to, always select the Clean now option when prompted at the end of a run. Also clean retorts after replacing reagent by

remote fill and drain, or if you filled the retorts using manual operations.

For most laboratories the pre-defined “Quick Clean” protocol should be the only cleaning protocol required. Under normal conditions the protocol purges residue in the retort to the wax bath before the first step (see (e.g. xylene) and cleaning alcohol. These are followed by a “dry step” that applies high temperature, vacuum and air flow to evaporate all reagent residue. At the end of the dry step the heaters turn off but air flow continues to cool the retorts before the next protocol.

Load and run cleaning protocols like other protocols, but never put tissue in the retort – the dry step will damage it. This means cleaning protocols should never be used for reprocessing runs – use a reprocessing protocol instead.

If required, copy the Quick Clean protocol and edit to create your own cleaning protocols. You can add, delete and edit all the reagent steps as for other protocols, but the dry step cannot be deleted or edited. Cleaning protocols do not require a water step and work well with conventional cleaning reagents.

Pre-cleaning Purges below). Then there are two reagent steps – cleaning solvent

Running Protocols

To completely remove xylene from your instrument, Leica Microsystems can supply Waxsol™, a xylene-free cleaning solution (see

WARNING

Remove all tissue from the retort before running a cleaning protocol as the dry step will damage the tissue.

WARNING

Do not use cleaning protocols for reprocessing as the dry step will damage the tissue.

CAUTION

Always run a cleaning protocol after wax has been in the retort.

CAUTION

Do not reuse contaminated dehydrants as cleaning alcohol. The contaminated dehydrants will contain formalin (or other fixatives) and the “dry step” will cause salts to crystallize on the retort’s internal surfaces.

5.1.4 Recommended Reagents).

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Running Protocols

Cleaning Laboratory Implements

You can clean metal laboratory implements such as cassette lids and metal molds during cleaning runs, but it is important to set reagent purity thresholds that take this into account.

All the pre-defined cleaning reagents have “cycle” purity thresholds. Under these the reagents must be replaced after ten or six cleaning runs (if they do not exceed a concentration threshold first). But the thresholds are designed for cleaning runs with only cassette baskets in the retorts – any additional material increases the rate that the cleaning reagents degenerate, requiring lower cycle thresholds. If you clean implements other than baskets lower the cycle thresholds for the reagents used, so the reagents are replaced more frequently (see

5.2.2 Editing Active Reagent Types). Depending on the number of implements you typically place in the retorts you may need to reduce the thresholds by half or more. Contact your technical support representative for advice if required.

CAUTION

If you clean laboratory utensils, metal cassette lids, metal molds etc. in cleaning runs lower the cycle purity thresholds for the cleaning reagents used. Failure to do so can lead to overly contaminated cleaning reagents and lower quality cleaning.

Modifying Cleaning Protocols for Different Retort Residues

Always run a complete cleaning protocol as soon as possible if wax or clearing reagent are left in the retorts.

For alcohol residue skip the first step of the protocol to start at the alcohol step (see 3.4.2 Editing the Protocol for a Single Run).

A residue of clean formalin can be allowed to stay in a retort if the next processing protocol begins

with a formalin step. If you are left with formalin in a retort at the end of a protocol tap Clean later when prompted, to continue without cleaning. If you need to clean a retort with formalin

residue in it, start the cleaning protocol with the alcohol step, as for alcohol residue.

Pre-cleaning Purges

Cleaning protocols are generally run to clean wax residue from the retorts, as wax is the final step of processing protocols. To help maximize the useful life of the cleaning solvent, the instrument usually purges any wax residue from the retort to the wax chamber it came from before the cleaning protocol begins.

If you attempt to load a processing protocol to a retort with incompatible residue you are warned with event 10011, “Incompatible reagent in retort. Clean retort or edit protocol.” A cleaning protocol run after this warning will not have the normal purge to the wax chamber. This is in case fresh cassettes were placed in the retort, contaminating the wax residue with formalin. A purge under these conditions would contaminate the wax chamber with formalin.

If you ever place fresh cassettes into a dirty retort in preparation for processing, remove the cassettes and then attempt to load a processing protocol before loading the cleaning protocol. The 10011 warning raised when you attempt to load the processing protocol causes the cleaning protocol to skip the wax bath purge. The retort residue, now with formalin in it, will not go into the wax bath but into the cleaning solvent.

After the cleaning protocol finishes replace the cleaning solvent, which will now be contaminated with formalin.

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In general, avoid this situation by always cleaning the retort immediately after a

Retort A Retort B

16 reagent bottles

4 wax chambers Retort B protocol panelRetort A protocol panel

Select/Unload

protocol:

button to load and

unload protocols for

retort A

Run/Pause

button for

retort A

Run/Pause button for retort B

Select/Unload protocol: 

button to load and unload protocols for retort B

processing run, when prompted. Do not put fresh cassettes into a retort that is showing residue in it, as indicated by the icon at right (formalin residue may be acceptable).

WARNING

3.3 Status Screen

Use the Status screen to run protocols and monitor protocol progress. The main features of the

screen are shown in

Figure 25.

Running Protocols

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Figure 25. Status screen

The central area of the screen shows the status of the stations and retorts. Panels at either side of the screen show protocols loaded for the retorts.

 3.3.1 Status Area

 3.3.2 Protocol Panels

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3.3.1 Status Area

Bottle number

Reagent type

Color-coded for

reagent group (see

Groups in 5.1.1

Reagent Groups, Types

and Stations for color

codes)

Reagent concentration (may not be visible,

see 6.1.2 Reagent

Management)

Hatched coloring

shows reagent is out of

threshold

Color or other pattern shows station state (see below)

The status area provides a visual guide to the status of the bottles, wax chambers and retorts, as shown below.

Bottle Icons

Running Protocols

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Figure 26. Bottle icons on the Status screen

Bottles have six possible station states:

Full In use Empty Dry No bottle Unknown

A reagent transfer is in progress or was abandoned. The reagent level is between

Means

The bottle holds sufficient reagent to fill a retort at the specified basket level.

full and empty.

Icon

The bottle has been used to fill a retort. There is still reagent in the bottle.

The bottle has been completely

The bottle has been

removed. drained leaving only a small amount of residue.

A previously missing bottle has been replaced. Enter reagent and state details before using this station.

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Wax Chamber Icons

Wax chamber number

Reagent type

(i.e. type of wax)

Color-code orange for reagent group “Wax”

Hatched coloring shows wax is out of threshold

Padlock symbol shows

there is a vacuum in

the chamber

Wax concentration (may not be visible,

see 6.1.2

Reagent Management)

Color or other pattern shows station state (see below)

The number of cassettes in

the retort

Retort name

Color-coded for reagent group

currently in the retort

Color or other pattern shows retort state (see below)

Current retort operation (see below)

Retort pressure, temperature, and stirrer speed (supervisors only)

Figure 27. Wax chamber icons on the Status screen

Wax chambers have four possible station states:

Means Icon

The chamber has enough wax to fill a retort

Full

to the specified basket level.

Running Protocols

Part full

Empty

Not molten

Retort Icons

A wax transfer is in progress or has been abandoned. The wax level is between full and empty.

The chamber has been drained to fill a retort. There is still wax in the chamber.

The wax in the chamber has not melted and is unavailable.

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Figure 28. Retort icon on the Status screen

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Running Protocols

There are ten operations reported for the retorts:

 Ready — the retort is available for any new action  Reserved — a protocol is loaded but has not yet started  Processing — the retort is currently running a protocol  Completed — the retort has completed the loaded protocol  Drying — the retort is being dried as the final step of a cleaning protocol  Filling — the retort is currently filling  Draining — the retort is currently draining  Pending (drain or fill) — the retort is waiting for resources to perform a fill or drain  Abandoning — the retort is abandoning the current action  Unavailable — the retort cannot be used, contact your service representative.

Retorts have five possible states:

Means Icon

The retort contains the correct amount of wax or reagent for the specified basket level.

Full

Part full

Empty

Clean

Retort inoperative

The reagent or wax level is between full and empty, this usually occurs during a fill or drain operation.

The retort is drained but contains residue.

There is no residue in the retort. This only occurs after a cleaning protocol.

A red cross over a retort indicates that a hardware failure has occurred and the retort is unavailable. Contact your service representative.

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3.3.2 Protocol Panels

Protocol name

Show details:

tap to expand protocol panel

Protocol finish time

Completed steps are checked

Progress through current step

Run/Pause: start a loaded protocol, or pause a running protocol (

see 3.5 Pausing and

Abandoning Protocols)

Select/Unload protocol:

load and unload protocols (disabled while

protocol is running)

Protocol steps

The station scheduled for the step

(a different station may be used)

Processing time: total time to run protocol

Protocol notes

Step duration, temperature, pressure/vacuum, and stirrer speed

Panels on each side of the Status screen show the steps of the protocols loaded for each retort.

Use the panels to load and unload protocols, initiate processing runs, and monitor protocol runs.

You can view the panels in two modes: standard and expanded (see images below).

Running Protocols

In expanded mode the protocol notes, processing time, and step details are also shown.

Figure 29. Protocol panel: standard mode

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Figure 30. Protocol panel: extended mode

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3.4 Protocol Run Options

Edit end time: change the end time for the run or set a new default end time for the retort

ASAP:

start the run as soon as

possible

–/+ Day: keep the current end time but change its day

Edit steps: Edit the protocol (

see 3.4.2

Editing the Protocol for a Single Run)

Start:

start the protocol run

Required end time:

the protocol end time you

have set

Predicted end time: the end time predicted by the Peloris system after scheduling

You can schedule each protocol run so it finishes at a convenient time. You can also modify the protocol for a run, to start at the second or later steps, and to change step durations.

 3.4.1 Scheduling Protocols

 3.4.2 Editing the Protocol for a Single Run

3.4.1 Scheduling Protocols

Schedule protocol runs in the Scheduling dialog box. The dialog box opens automatically for every protocol run after you have loaded the protocol, tapped Run, cleared any warning messages, and placed cassettes in the retort. When you tap Start in the Scheduling dialog box there are no

further configuration options or warnings and the protocol run starts.

The Scheduling dialog box also gives access to the Edit protocol instance dialog box where you

can edit some protocol features for the run (see

Running Protocols

3.4.2 Editing the Protocol for a Single Run).

Each retort (note, not each protocol) has a default scheduling setting. The Scheduling dialog box

always opens showing the retort’s default setting. You can accept the default or change the setting for the run with options to set a different end time or run the protocol as soon as possible (the

ASAP option). Also change the retort defaults from the Scheduling dialog box.

The system considers the required end time as the latest acceptable protocol completion time. To avoid resource clashes, protocols may be scheduled to finish earlier than the required end time. A red highlight indicates that the required end time is not possible and a later end time has been set.

The required end time for cleaning protocols is always set to ASAP.

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Always check the predicted end time to ensure it is suitable before starting a protocol.

Figure 31. The Scheduling dialog box

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Running Protocols

How To Schedule a Protocol Run

When the Scheduling dialog box opens the retort’s default end time is shown.

 If the default end time is set to ASAP the protocol is scheduled to end at the earliest possible

time.

 If the default setting is a specific time of day, the dialog box defaults to that time on the

following day.

You have four options:

1. Accept the default values as they are.

Edit the protocol for the run if required (see 3.4.2 Editing the Protocol for a Single Run) then

tap Start to begin the run.

2. Keep the default time but change the day the protocol will run.

Tap th e + day or – day button to keep the default end time but change the day.

If the default setting is a specific time of day the dialog box opens with the run set to the following day. To run the protocol on the current day tap the –

the time you do this the new end time may not be possible. If so, the Predicted end time is

highlighted red.

day button once. Depending on

3. Start the run as soon as possible.

Tap th e ASAP button.

The protocol will normally start immediately. However, if there is a reagent clash caused by a protocol running in the other retort the actual start of the protocol may be delayed (see Delayed End Times and Initial Fills).

4. Set a new end time.

Tap th e Edit end time button to open the Run protocol – edit end time dialog box (see

the next section for instructions).

3.6.1

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Running Protocols

Keypad to enter time in top

field above.

Use 24 hour clock.

Scheduled time of day

Scheduled day

ASAP: Use if setting the “as soon as possible” option as the retort default

–/+15: change the scheduled time of day in 15 minute increments

–/+ Day: change the scheduled day

Set as default: Set the time of day currently entered or “as soon as possible” setting as the retort default

Entering a New End Time or Default Scheduling Setting

Change the end time for a specific run in the Run protocol – edit end time dialog box, opened from the Scheduling dialog box with the Edit end time button.

Also set the default scheduling setting for the current retort in the Run protocol – edit end time

dialog box.

 To set a new end time for a protocol run use the keypad to enter the required end time of day

 To set a new retort scheduling default enter a time of day (as you would to change the end

Figure 32. The Run protocol – edit end time dialog box

(24-hour format) or use the –15 or +15 buttons to increment the time in 15 minute steps. Use the + Day and – Day buttons to change the day. Tap OK when finished.

time for an individual run) or tap ASAP. The day is not relevant to the default setting. Tap Set as default then OK.

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3.4.2 Editing the Protocol for a Single Run

No check in the circle shows

this step will be skipped

Tap the step that will be the

first to run in the protocol

Tap on a step time to open the Duration dialog box to set a new step duration

You can edit the protocol for an individual run just before the run is started. You can make two types of change:

1. Skip the first steps of the protocol

2. Change step durations

Make both types of change in the Edit protocol instance dialog box opened from the Scheduling dialog box. Start a protocol run as normal from the Status screen and continue until the Scheduling dialog box opens. Tap the Edit steps button to open the Edit protocol instance

dialog box.

Running Protocols

 To skip protocol steps tap the step that you want to start the run with. Steps prior to this are

 To change a step time tap the current step time. Set a new time in the Duration dialog box.

Skipping steps and changing step durations will affect protocol scheduling – confirm that the new

Predicted end time shown in the Scheduling dialog box is acceptable before you start the run.

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Figure 33. Edit protocol instance dialog box

unchecked to show they will not run.

The reagent selected as the new first step will be used for an initial fill if required (see 3.6.1 Delayed End Times and Initial Fills).

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3.5 Pausing and Abandoning Protocols

Emergency stop:

abandon protocols in both

retorts

5-minute count down – if you do not select an option within 5 minutes processing automatically resumes

Abandon: abandon the protocol running in the retort. The protocol in the other retort will resume.

Access retort:

prepare the retort to allow you

to open it, e.g. to add more

cassettes

Resume:

continue processing in both

retorts

Vent wax: vent the wax chambers to allow you to open them

Abandon and Access retort buttons for retort B

Abandon and Access retort

buttons for retort A

To stop a protocol that has started use one of the Pause buttons on the Status screen protocol panels. When you tap either Pause button protocols in both retorts stop running, and the Paused

dialog box opens with a number of options:

 Abandon all processing or just the protocol in one retort.

 Access a retort, for example to add more cassettes, and then resume the protocol running in it.

 Vent the wax baths so you can open them.

After you pause the instrument you have five minutes to select an option, after which processing automatically resumes.

Running Protocols

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Figure 34. Paused dialog box

WARNING

Take care if opening a retort or wax chamber after pausing the instrument. Retorts may contain very hot fluid that could cause severe burns, and hazardous reagents and vapors. Read any warning messages, e.g. if the retort is above safe access temperature, and take appropriate precautions before continuing.

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Running Protocols

Emergency Stop and Abandon

After you have paused the instrument you can abandon all protocols with the Emergency stop

button. Note that this does not shut down or remove power from the instrument (see

2.1 Switching

On and Shutting Down).

Alternatively, abandon the protocol run in one retort only with the appropriate Abandon button.

Any protocol running in the other retort will resume.

When processing stops the Peloris goes through the same routines carried out at the end of a normal protocol run. It prompts you to drain the retort (if full), remove cassettes, and run a cleaning protocol.

After abandoning a protocol you may wish to run a reprocessing protocol to recover your cassettes. In this case do not remove your cassettes or run a cleaning protocol when prompted to do so.

If the last reagent was a fixative you may skip the cleaning protocol as the residue will not prevent you running a typical processing protocol. If you decide to run a cleaning protocol, set the first step to a cleaning alcohol. Cleaning solvents are incompatible with fixatives.

Access Retort

You can access retorts in a paused instrument in order to add or retrieve samples.

CAUTION

Take care when adding fixed samples to a running protocol. The additional fixative will contaminate the reagent used in the current step and this contamination will not be tracked by the reagent management system.

CAUTION

The further a protocol has progressed before you add more samples the more compromised the processing quality for those samples. We therefore recommend that you only add samples during fixative steps or during the first dehydrant step.

To access a retort while the instrument is processing:

1. Pause the instrument with one of the Pause buttons on the Status screen.

2. Tap the appropriate Access retort button in the Paused dialog box.

3. Select to drain the retort or not in the Temporary access drain dialog box.

Follow the prompt to wait if draining.

4. When the Retrieve samples dialog box opens remove the baskets from the retort and add or

retrieve cassettes, as required.

5. Return the baskets to the retort and tap OK in the Retrieve samples dialog box.

6. If prompted, enter the new number of cassettes in the Number of cassettes dialog box.

Follow the prompt to wait if refilling the retort.

7. Tap Resume in the Paused dialog to resume the protocol.

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3.6 Retort Scheduling

The Peloris tissue processor allows you to simultaneously run protocols in both retorts. The automatic scheduling function attempts to assign reagent stations and start times so that there are no clashes and it may alter your requested end time by starting the protocol early or by inserting a delay time (see

Also, when starting a second protocol you may notice that the reagent stations assigned when a protocol was loaded change as it begins to run. This occurs when the instrument must alter the assignment to allow for the first protocol’s current reagent requirements.

It is sometimes not possible to schedule a second protocol. This situation and possible remedies are discussed in station unexpectedly becomes unavailable. 3.6.3 Unavailable Reagents describes the best ways to avoid this situation.

3.6.1 Delayed End Times and Initial Fills

Protocols do not need to start immediately and it is possible to set a required end time that necessitates a delay before the actual protocol begins. This delay period can extend to many days. Also, when selecting the ASAP (As Soon As Possible) scheduling option, or if you have requested an end time that is not achievable, the Peloris tissue processor may be forced to delay the start of the protocol. During the protocol delay period the Peloris tissue processor will protect your cassettes by covering them with reagent; this process is called an initial fill.

3.6.1 Delayed End Times and Initial Fills).

3.6.2 Unavoidable Reagent Clashes. Also, protocols will sometimes fail if a reagent

Running Protocols

During the initial fill, the retort is filled with the first scheduled reagent (usually a fixative) to protect the samples. Unless the reagent is wax no heating or agitation occurs. If the initial step is wax (for reprocessing or wax only protocols), the retort temperature will be set to wax standby, and the stirrer will be set to the first step’s speed. Once the initial fill period is over the protocol will run normally and will finish at the predicted end time.

We recommend that all protocols start with a fixative step (even if only very short) so that a fixative is used for any initial fill. If there is no fixative step, an initial fill may leave your tissue covered with dehydrant for a long period and this can cause the tissue to become hard and brittle.

3.6.2 Unavoidable Reagent Clashes

Unavoidable clashes often occur when there are insufficient reagent stations available for both protocols to satisfy the reagent selection rules (see more frequently when using “by type” and “by station” protocols as they have limited station assignment flexibility.

Always ensure sufficient stations of the first reagent group or type so a station is available for an initial fill.

4.1.2 Reagent Selection Method). This occurs

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3.6.3 Unavailable Reagents

Once a protocol starts, group and type select protocols may reassign stations to recover from errors caused by unavailable reagents (for example when a bottle is removed or if a station contains insufficient reagent). This reassignment may use reagents assigned to the other protocol.

Station-selection protocols will fail if an assigned reagent becomes unavailable. Type-selection protocols will fail if there is only one station with an assigned type and it becomes unavailable.

Some common causes of station unavailability, and ways to avoid them, are described below.

 The station contains insufficient reagent.

Prior to each run, check the reagent level in each station is sufficient for the current fill level

(see Instrument settings screen for the reagent fill level).

 A bottle scheduled for use is removed from the reagent cabinet.

For safety reasons you should not remove any bottle whilst a protocol is running. However if you choose to do so, you must make sure the bottle you intend to remove is not scheduled for use in either retort.

 A wax station is not molten at the time it is required.

Make sure there is adequate time for the wax to melt and that the correct wax station state is set (see

5.3.2 Setting Reagent Station Properties).

Running Protocols

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Protocol Setup

Protocols control all aspects of the tissue processing runs carried out on the Peloris. This chapter gives an overview of Peloris protocols and how to create, edit and view protocols with the software interface.

 4.1 Protocol Overview

 4.2 Creating, Editing and Viewing Protocols

4.1 Protocol Overview

Protocols consist of sequences of steps applied to tissue in a retort. In each step (with one exception) the retort is filled with reagent and held for a time under conditions controlled by the protocol. Protocol steps have the following properties:

 the reagent used

 the time the reagent is in the retort

 the temperature of the reagent

 the retort pressure: ambient, pressurized or vacuum, or cycling between pressurized and

vacuum

 the retort stirrer speed

 the drip time: the time allowed for reagent to drip from the cassettes and retort walls before

ending a drain. Longer drip times reduce carryover.

The one step type that is an exception is the final “dry” step of a cleaning protocol, where no reagent is used.

There are five protocol types. A protocol’s type sets limits on which reagents can be used and the order of their use.

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Other protocol properties are the reagent selection method and a carryover value that must be set for each protocol. These, and protocol validation, pre-defined protocols and file saving are described in the sections below.

 4.1.1 Protocol Types

 4.1.2 Reagent Selection Method

 4.1.3 Pre-defined Protocols

 4.1.4 Protocol Validation

 4.1.5 Carryover Setting

 4.1.6 Saving Protocol Files

4.1.1 Protocol Types

The Peloris tissue processor uses five protocol types for different processing functions. The protocol types allow different reagent sequences and temperature ranges (see Tab le s and 8.4 Protocol Step Temperatures). Once a protocol is created you cannot change its type.

The protocol types are:

Protocol Setup

8.5 Reagent Compatibility

 Standard — conventional tissue processing sequences using a clearer such as xylene. Suitable

for normal processing requirements. These protocols can be constructed with or without defatting steps.

 Standard reprocessing — to recover under-processed tissue on an instrument configured for

standard processing. These protocols start with cleaning reagents before moving to a standard tissue processing sequence.

 Xylene-free — protocols with high temperature wax steps and advanced processing

techniques to process tissue without conventional clearing steps. Suitable for normal processing requirements.

 Xylene-free reprocessing — to recover under-processed tissue on an instrument configured

for xylene-free processing. These protocols start with cleaning reagents before moving to a xylene-free tissue processing sequence.

 Cleaning — protocols to clean the retorts and reagent lines. Always run a cleaning protocol as

soon as possible after wax has been in the retort. See

3.2 Cleaning Protocols for further

information.

See Protocol Icons in 4.2.1 The Protocol Selection Screen for the icons used for each protocol type.

Note the following points:

 Xylene-free reagent selection — xylene-free protocols use two sets of dehydrants rather

than dehydrant followed by clearer, as used in standard protocols. This means xylene-free protocols cannot use group reagent selection (see 4.1.2 Reagent Selection Method).

 Xylene-free baskets — always use spaced cassette baskets for xylene-free protocols.  Reprocessing carryover — during reprocessing protocols there is significant reagent carry-

over following the cleaning stages. After running a reprocessing protocol you should replace the first three processing reagents that are used after the last cleaning reagent.

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4.1.2 Reagent Selection Method

All protocols use one of three reagent selection methods: group, type or station (see 5.1.1 Reagent Groups, Types and Stations for definitions of these terms). Once a protocol is created you cannot change its reagent selection method.

A protocol’s reagent selection method determines the way the system selects reagent stations when the protocol is run. With the station selection method you define exactly the station to use for each step, so the system makes no “choices”. For group and type selection the system selects a station from a number that are available to it, to get the best concentration for the protocol step (see Station Selection Rules below). In summary:

 Group selection — the system selects from all stations with reagent of the group defined for

the protocol step. A station’s reagent name (its type) is not used for selection, only the reagent group and concentration.

For example, if you have bottles with reagent types “Ethanol 70%” and “Ethanol 90%” on the instrument, the system will pick an “Ethanol 90%” bottle for the first dehydrant step if that bottle has the lowest (in-threshold) concentration. Both reagent types are dehydrants, so are equal candidates for dehydrant steps.

 Type selection — the system selects from all stations with reagent of the type defined for the

protocol step. Station reagent names (i.e. types) and concentration are used for selection.

Using the example above, with “Ethanol 70%” and “Ethanol 90%” bottles on the instrument, if the first dehydrant step in the protocol specifies “Ethanol 70%” then the Ethanol 70% bottle with the lowest (in-threshold) concentration will be used, even if there is an Ethanol 90% bottle with lower concentration. Because Ethanol 70% and Ethanol 90% are different reagent types the system does not consider them both.

Protocol Setup

 Station selection — the system uses the stations defined in the protocol (typically, users

define the bottles in order: bottle 1 first, then bottle 2, 3, etc.). Stations are defined by number, so the name of the reagent in a station (its type), nor the reagent group are used for selection.

Again using the example above, if there are two Ethanol 70% bottles on the instrument and the first dehydrant step of the protocol is configured to the first of these bottles, that bottle will be used regardless of the concentration of reagent in the other bottle.

Station Selection Rules

The system uses the following rules to select stations for protocols with group and type reagent selection. “Sequence”, as used below, means a series of protocol steps using the same reagent group or reagent type.

 The first step of a sequence uses the lowest concentration station available.

 The last step of a sequence uses the highest concentration station available.

 Intermediate steps in a sequence use the lowest concentration station that has not already

been used.

 Where there is a single step for a particular reagent group or type the highest concentration

station is used.

 Stations that have exceeded any of their use thresholds (and are not locked out) are not

selected unless there is no other station available.

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Protocol Setup

Reagent Selection Methods Compared

When creating protocols decide which method best suits your processing needs and reagent management strategy. Note, however, that xylene-free protocols cannot use group selection. Xylene-free protocols use dehydrants for two different functions and group selection cannot differentiate these.

Group selection ensures optimal reagent selection with minimal management. You get maximal use from reagents and with the widest range of stations to select from scheduling conflicts are minimized. You must however take some care when using group selection as the Peloris tissue processor may use a reagent type you wished to reserve for a particular purpose. In these cases use the type or station selection method or, for one-off instances, temporarily block a station by setting its state to “In use” (see

Type selection offers the same sorts of benefits as group selection – optimal selection of reagents according to concentration, minimal reagent management, efficient reagent use, and minimal scheduling conflicts. However, (provided there is more than one reagent type per group) the system selects from a smaller range of stations, so the benefits are lessened. On the other hand you have greater control over reagent selection.

Station selection gives you total control over reagent selection. However, as reagents degrade, you need to rearrange bottles between protocols if you want to ensure the most suitable reagents are used. This is a significant management burden that opens the possibility for errors. Also, the station select method does not allow the instrument any flexibility when scheduling protocols and it will not be able to recover from a processing error caused by unexpected reagent unavailability.

Setting Station States in 5.3.2 Setting Reagent Station Properties).

Station selection protocols are not recommended for overnight processing. If a reagent becomes unavailable for any reason then the protocol cannot be completed.

When running station selection protocols always check the concentration of the assigned stations before starting a run as the concentrations may not be correctly ordered if other protocols have run.

Your decision about the reagent selection method must be made in combination with decisions about how many, and which, reagent types you use, and the concentration thresholds to set for these. Note that all the pre-defined protocols in the Peloris system use type selection but with recommended bottle configurations that have the minimal number of reagent types (see of Pre-defined Protocols and 8.3 Station Configurations). This combination provides a system that is similar to group selection, with all the consequent benefits.

4.1.3 Pre-defined Protocols

Each Peloris system includes 11 pre-defined protocols – 1, 2, 4, 8 and 12 hour protocols for standard and xylene-free processing, and a cleaning protocol (see

Protocols). Access the pre-defined protocols from the Protocol selection screen by selecting New and then selecting the Pre-defined icon.

The pre-defined protocols are designed for use with the bottle configurations described in 8.3 Station Configurations. Leica Microsystems has extensively tested the protocols and found they give excellent results (in combination with proper reagent management and instrument maintenance). However, users should validate all protocols, including the pre-defined protocols, for use in their laboratories, where different conditions could give different outcomes.

8.2.2 List

8.2.2 List of Pre-defined

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Pre-defined protocols can be copied to appear in the Protocol selection screen where they

become available for use. They can be copied as they are, even keeping the name unchanged, or once copied you can modify them to suit your purposes. The original versions cannot be changed. See

Copying Protocols in 4.2.3 Creating New Protocols for directions to copy a pre-defined protocol.

In new Peloris systems the pre-defined protocols are all provided, ready for use, in the Protocol selection screen. In case these versions are edited or deleted, however, the original versions remain available under the Pre-defined icon accessed with the New button.

4.1.4 Protocol Validation

Supervisors creating or editing protocols (or copying pre-defined protocols) have the option to “validate” them in the Peloris software. This serves as a sign that the protocols have passed the laboratory’s validation tests and can be used for regular clinical processing. Supervisors can also make valid protocols invalid.

Protocols that have been marked as valid can be run by operator-level users, while invalid protocols cannot. Invalid protocols can be run by supervisors.

Icons for validated protocols have a green check, while the icons for invalid protocols have a red cross:

Protocol Setup

Figure 35. Icon for a valid protocol Figure 36. Icon for an invalid protocol

Set protocol validity status on the Edit protocol screen, with the Validate protocol / Invalidate protocol button.

4.1.5 Carryover Setting

The Carryover setting is a protocol setting for the additional carryover due to biopsy pads and

other small-tissue carriers.

This section has, first, a general overview of carryover in the Peloris system, then describes how to

use the Carryover setting in particular.

Carryover – Overview

When reagent drains out of a retort and is replaced with reagent from another station a certain amount of the first reagent remains in the retort and mixes with the new reagent. The Peloris reagent management system calculates the amount of this “carryover” and uses it to determine reagent concentrations.

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Protocol Setup

Carryover has three main components:

 Reagent on retort walls and baskets

 Reagent on cassettes, and on and infiltrated into tissue

 Reagent on and infiltrated into small-tissue carriers (e.g. biopsy pads, biopsy cassettes, wraps

etc.).

The reagent management system automatically calculates the carryover on retort walls and baskets, taking into account the retort fill level and drip time.

The carryover due to cassettes and tissue is calculated using the number of cassettes entered by users at the start of each run (in some cases an average number of cassettes may be used, see

6.1.2 Reagent Management). The amount of carryover on a standard cassette is used in the calculation. Drip time is also included.

The reagent management system calculates carryover from small-tissue carriers using the protocol

Carryover value you set.

Carryover values are on a scale from 0 to 100:

 A setting of 0 indicates that there is no carryover due to small-tissue carriers like biopsy pads,

i.e. the run has only standard cassettes with no small-tissue carriers.

 A setting of 100 indicates there is carryover equivalent to having all the tissues in a run using

biopsy pads (biopsy pads have the maximum carryover of all small-tissue carriers).

Because biopsy pads can have up to 10 times the carryover of standard cassettes it is important to

set a truly representative Carryover value in your protocols (as it is to accurately enter the number of cassettes in each run). If you set too high a Carryover value the system calculates too rapid

degradation of reagents and requires you to replace them sooner than necessary. With too low a setting the system calculates that reagents are more pure than they are. You will use reagents beyond their optimal effectiveness resulting in poor processing quality.

Protocol carryover values are set by supervisors on the Edit protocol screen (the default value is set on the Reagent management screen). Tap the Carryover button and enter a number

between 0 (no carryover from small-tissue carriers) and 100 (maximum carryover from small-tissue carriers).

How to Calculate Carryover Values

Carryover is dependent on the types of cassettes and other small-tissue carriers used: e.g. biopsy pads, paper or tissue inserts, mini cassettes, biopsy cassettes etc. It also depends on the proportion of these in each run.

The carryover setting is a protocol property, so it must be set to the average carryover value for runs that use the protocol.

The following table shows the carryover values that should be used for a range of cassettes and pads etc. provided by Leica Microsystems. The values in the table apply when all the tissue in the

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run uses the respective cassette or pad type.

Leica Microsystems products Generic description of tiss ue carrier

Protocol Setup

Carryover value if 100% of tissue uses carrier

Surgipath® ActivFlo™ Routine I

Surgipath Biopsy Pads in 

Standard cassette 0

Biopsy pad in standard cassette 100

Surgipath ActivFlo Routine I

ActivFlo Mini Cassette in 

Mini cassette in standard cassette 50

Surgipath ActivFlo Routine I

Surgipath Biopsy Wraps in 

Biopsy wrap in standard cassette 20

Surgipath ActivFlo Routine I

Surgipath IP ActivFlo Biopsy I

Biopsy cassettes with >1 mm pore size 0

McCormick™ MC-605

Sample Calculation

The average run of a protocol uses the following proportions of tissue carriers:

 Surgipath ActivFlo Routine I: 40%

 Surgipath Biopsy Wraps in Surgipath ActivFlo Routine I: 60%

Multiply the proportion of each carrier with its value from the table above to calculate the additional carryover value for that carrier:

 Surgipath ActivFlo Routine I: 40% × 0 = 0

 Surgipath Biopsy Wraps in Surgipath ActivFlo Routine I: 60% × 20 = 12

Add the resulting values:

 0 + 12 = 12

Enter a carryover value of 12 for the protocol.

Peloris software versions before version 1.40 had a “Biopsy pad” setting for small-tissue carrier carryover. Users with satisfactory “Biopsy pad” settings in those versions should use the same

numeric value for the Carryover setting.

Other Products

For small-tissue carriers other than those in the table above we recommend you start with a carryover setting of 50. Use your own observations of tissue and reagent quality to refine this value. Tissue shrinkage in the block and excess solvent in the wax bath might both be indications that you have too low a carryover setting.

It is users’ responsibility to validate the carryover settings in their protocols.

Contact your technical support representative if you require assistance setting suitable carryover settings.

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4.1.6 Saving Protocol Files

Protocol icons

Load button: load selected protocol

Selected protocol

Invalid protocol

Protocol creation and editing buttons – Operators use View button to view protocol configurations

Protocols are saved in “cfg” extension files that you can back up or to send to your service representative for troubleshooting. See to copy protocol files on and off the instrument.

Transferring Protocols in 6.2.7 File Transfer for instructions

4.2 Creating, Editing and Viewing Protocols

Supervisors can create and edit protocols from the Protocol selection screen. Operators cannot create or edit protocols, but can view protocol details from the Protocol selection screen.

 4.2.1 The Protocol Selection Screen

 4.2.2 Editing Protocols

 4.2.3 Creating New Protocols

 4.2.4 Viewing Protocols

Protocol Setup

4.2.1 The Protocol Selection Screen

Tap th e Protocols button in the Function bar to open the Protocol selection screen where you

access all protocol configuration options.

Figure 37. The Protocol selection screen

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Protocol Setup

Protocol name

Reagent selection method

(

see 4.1.2 Reagent Selection

Method)

Protocol duration

Validation status (

see 4.1.4

Protocol Validation)

Protocol type indicated by icon pattern and color (see below)

Protocol Icons

On the Protocol selection screen each protocol is represented by a selectable icon. Each icon

contains the following protocol details:

Figure 38. Protocol icon

Icons for the five protocol types (see 4.1.1 Protocol Types) have different background patterns and colors as shown below:

Standard (white) and Standard Reprocessing (white with red stripe) Cleaning (blue)

Xylene-free (green) and Xylene-free Reprocessing (green with red stripe)

4.2.2 Editing Protocols

To edit an existing protocol open the Protocol selection screen, select the protocol, then tap Edit to open the Edit protocol screen.

Steps can be added and removed and step details – time, temperature etc. – changed. The protocol’s name, notes, carryover setting and validation status can all be changed. You cannot change the protocol type or reagent selection method. You cannot remove the dry step from a cleaning protocol.

Only supervisors can edit protocols.

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Figure 39 and Figure 40 show the Edit protocol screen and describe its use.

Each row represents a

protocol step

Cells in the step table show the settings for reagent, time, temperature, pressure or vacuum (P/V), stirrer speed, and drip time for each step.

Tap a cell to open a dialog box to change the setting.

Selected step:

tap the step number to

select a step

Protocol icon: updates as protocol is edited

Protocol type (cannot change)

Protocol configuration buttons (see Figure 40 below for details)

Insert:

tap to insert a new step above the

currently selected step

Delete:

tap to remove the currently

selected step from the protocol

Name: change the protocol name

Notes: enter a description or other notes for the protocol

Carryover: set the carryover value (

see 4.1.5 Carryover

Setting)

Validate/Invalidate protocol: set the protocol as valid or invalid (

see 4.1.4 Protocol Validation)

Save: save changes made to the protocol

Figure 39. Edit protocol screen

Protocol Setup

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Figure 40. Configuration buttons on the Edit protocol screen

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Protocol Setup

Tap anywhere on the group

button to select the reagent

group

Show compatible: show only compatible reagent groups

Show all: show all reagent groups

Tap on a type button to select

the reagent type

Show compatible: show only compatible reagent groups

Show all: show all reagent groups

Selecting Reagents

When you select the Reagent cell in the protocol step table to add or change a reagent the dialog box you see depends on the reagent selection method.

For all the methods you can show only reagents that are compatible with the preceding protocol step (for the protocol’s type), or all reagents. For station selection you can hide stations that have already been selected. If you choose an incompatible or hidden reagent it is added to the protocol table with an asterisk to indicate that it is disallowed. You cannot load the protocol or run the protocol.

Group Reagent Selection

If the protocol uses group reagent selection you can see the protocol types configured for the instrument, but can only select by group.

Type Reagent Selection

If the protocol uses type reagent selection you can see the protocol types configured for the instrument, ordered by group. Select specific types.

Figure 41. Reagent selection – Group dialog box

Figure 42. Reagent selection – Type dialog box

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Protocol Setup

This station is “hidden”

because it has already been

used for a previous step

Hide used: show stations that have already been selected as unavailable

These stations are unavailable because they are not compatible with the preceding protocol step

These stations are available

for selection

Show compatible: show only compatible stations as available

Show all: show incompatible stations as available

The wax chambers are all unavailable because they are not compatible with the preceding protocol step

Station Reagent Selection

If the protocol uses station reagent selection you can see the stations configured for the instrument. Bottles that are available for selection are drawn in 3D with lids and handles. Bottles that are not available, because they have already been used or are incompatible, are drawn in 2D without lids or handles. Wax stations are similarly drawn as 3D buttons (available) or 2D icons (unavailable). Select specific stations for your protocol.

Deleting a Protocol

To delete a protocol select the protocol icon on the Protocol selection screen and tap Delete.

Pre-defined protocols can be restored if required, with the normal protocol creation procedure. Other protocols cannot be retrieved unless you have copied them to an external device using the file transfer functions (see

Figure 43. Reagent selection – Station dialog box

6.2.7 File Transfer).

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4.2.3 Creating New Protocols

Create new protocols from scratch or copy an existing or pre-defined protocol to modify. Make sure you select the right protocol type and reagent selection method when you start (or copy a protocol of the right type and reagent selection method) because these settings cannot be changed after you have started protocol configuration.

WARNING

Instructions below describe how to create new protocols from scratch. See Copying Protocols below for instructions to create a new protocol by copying another one.

Creating New Protocols From Scratch

1. Open the Protocol selection screen (Protocols in the Function bar) and tap New.

2. Select the protocol type (see 4.1.1 Protocol Types)

see 4.1.4 Protocol Validation). Use of nonvalidated protocols may

Protocol Setup

3. Select a reagent selection method (see 4.1.2 Reagent Selection Method)

Automatic dialog boxes will now guide you through the creation of the first step.

4. Tap the next row in the protocol table to add the second step.

You are prompted to supply the reagent and step duration – other step properties (pressure, stirrer etc.) are inherited from the previous step. Tap the appropriate cell to change any of these values.

Cleaning protocols automatically have a final dry step. You cannot edit this step.

5. Add further steps as required.

6. Tap the Name button to name your protocol.

7. Optionally tap the Notes button to add any information you want to keep with the protocol.

8. Set a carryover value with the Carryover button (see 4.1.5 Carryover Setting).

9. Tap the Save button to save the protocol.

10. Tap the Done button to finish.

Your new protocol will now be available in the protocol selection list.

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Protocol Setup

Copying Protocols

You can copy any protocol displayed on the Protocol selection screen in order to create a new

one based on it. Alternatively copy a pre-defined protocol.

1. Open the Protocol selection screen (Protocols in the Function bar) and: (i) select a protocol to copy on the Protocol selection screen

(ii) tap the New button and then the yellow Pre-defined icon. Then select the pre-defined

protocol to copy.

2. Tap the Copy button from the control panel.

3. Use the keypad to enter a new name for your protocol.

The Edit protocol screen opens with the copied protocol.

4. Modify the protocol as described in 4.2.2 Editing Protocols.

You cannot edit the final dry step in cleaning protocols.

5. Tap the Save button to save the protocol.

6. Tap the Done button to finish.

Your new protocol will now be available in the protocol selection list.

4.2.4 Viewing Protocols

Operator-level users cannot create or edit protocols. However they can view all protocol details including step details, notes, and the date and time the protocol was last modified.

To view a protocol’s details select the protocol icon on the Protocol selection screen (Protocols on the Function bar) and tap the View button.

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Reagent Setup

This chapter gives an overview of Peloris reagent management as well as providing instructions to replace reagents and configure them in the software.

 5.1 Reagents Overview

 5.2 Managing Reagent Types

 5.3 Managing Reagent Stations

 5.4 Replacing Reagents

5.1 Reagents Overview

Using the right reagent at the right time, at the right concentration, is of utmost importance for high quality tissue processing. The Peloris system has an advanced reagent management system that helps ensure consistently high quality processing while allowing you flexibility to fit into your laboratory’s workflows.

The Reagents Overview section describes the main features of reagent management in the Peloris system:

 5.1.1 Reagent Groups, Types and Stations

 5.1.2 Concentration Management

 5.1.3 Thresholds

 5.1.4 Recommended Reagents

 5.1.5 Tissue Marking

 5.1.6 Reagent Compatibility

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5.1.1 Reagent Groups, Types and Stations

The Peloris tissue processor manages reagents by groups, types and stations.

Groups

Groups specify reagent function. For example, the fixatives reagent group includes all reagents that can be used as a fixative.

There are nine factory-defined groups. Each group has a color-code used in the Peloris software and on bottle labels. Refer to the following table for a list of the groups and their colors and functions.

Group Function Color

Fixatives Tissue preservative. Green

Dehydrants Removes fixative reagents from tissue. Blue

Defat Removes fat deposits from tissue. Yellow

Post defat The dehydrant used after a defatting step. Purple

Clearers Clears the dehydrants from the tissue. Pink

Wax The embedding medium. Orange

Cleaning solvents First cleaning reagent. Light pink

Cleaning alcohols Second cleaning reagent. Light blue

Cleaning water Third retort cleaning reagent. Grey

Reagent Setup

The reagent group determines reagent compatibility (see 5.1.6 Reagent Compatibility).

Types

Reagent types are the specific reagents within each group, e.g. formalin, xylene, Waxsol. As well as the chemical constituent, reagent type definitions can include concentrations. For example “70% Ethanol” and “80% Ethanol” are reagent types defined in Peloris.

Reagent types have the following properties:

 A unique name

 Default concentration: the concentration of the reagent when fresh.

 Purity thresholds: to ensure you replace degraded reagent (see 5.1.3 Thresholds).

 Temperature thresholds: used to ensure processing quality and safe usage of the reagent (see

5.1.3 Thresholds).

The Peloris software includes a number of pre-defined reagent types. These are adequate for most laboratories, however you can create your own reagent types if needed.

Use the Reagent types screen to define and edit reagent types (see 5.2 Managing Reagent

Type s).

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Reagent Setup

Reagent type names do not affect reagent concentration. For example, when assigning a reagent type called “Ethanol 70%” to a station, the initial concentration value would be the type’s default value (probably 70%) but you could set the initial concentration to anything between 0 and 100%.

Stations

The Peloris tissue processor has 20 reagent stations: the 16 reagent bottles and the 4 wax chambers.

Each station has the following properties:

 The reagent type that the station contains

 The concentration of the reagent in the station, as calculated by the Peloris system

 The station’s use history:

 The number of cassettes processed with the reagent in the station

 The number of runs (cycles) processed with the reagent in the station

 The number of days the reagent has been in the station

 The station’s state:

 Dry: the station has been completely drained leaving only a small amount of residue. It

can be filled with any reagent.

 Empty: reagent has been removed from the station to fill a retort. Reagent in excess of

the amount needed to fill the retort remains in the station.

 In use: a reagent transfer is in progress or has been abandoned.  Full: the station holds enough reagent to fill a retort.  Not molten: for wax chambers only, the state to set when adding solid wax (see 5.4.5

Replacing Wax).

 For wax chambers only, the chamber’s current temperature.

Use the Reagent stations management screen to define reagent stations and to monitor their

use history and concentration (see

5.3 Managing Reagent Stations).

5.1.2 Concentration Management

The high quality tissue processing delivered by the Peloris system is largely due to its accurate monitoring of the concentration of the reagents in each station. This section describes the main features of concentration management in the system.

Concentration in the Peloris System

Concentration is the proportion of a reagent that is of the group to which the reagent is assigned. The following examples illustrate how the concentration is determined.

 A dehydrant that is 80% ethanol (a dehydrant) and 20% water (not a dehydrant) has a

concentration of 80%.

 A dehydrant that is 80% ethanol (a dehydrant) and 20% IPA (also a dehydrant) has a

concentration of 100%.

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Reagent Setup

 Absolute ethanol (100% dehydrant) contaminated by carryover from absolute IMS (100%

dehydrant) has a concentration of 100%, as both the original reagent and the contaminant are dehydrants.

 A new xylene (100% clearer) contaminated by carryover from absolute ethanol (100%

dehydrant) has a reduced concentration — typically around 94% after one cycle — as it will consist of 94% xylene (clearer) and 6% ethanol (not a clearer).

A reagent that is used early in a sequence of the same group will have a rapid concentration decline as most of the contamination it receives will be from the previous group. A reagent that is used late in a sequence will have a slow concentration decline as most of the contamination it receives will be from the same group.

Managing Concentrations

The Peloris software uses reagent concentrations to select stations when protocols are run (unless the protocol uses station reagent selection). It selects the station with the lowest (in-threshold) concentration of a reagent group or type for the first step using that group or type, then stations of increasing concentration for following steps. It always uses the highest concentration reagent for the last step before changing to another reagent group or type. The software also uses concentration information (amongst other factors) to prompt you to change reagents that have exceeded purity thresholds.

It is very important, then, for high quality processing and efficient reagent use, that the concentration information the software uses is accurate. The software automatically tracks the concentration of the reagent in each station, updating values after each run. For it to do this effectively you must enter accurate information for it to work with, e.g. set realistic protocol carryover values and enter the correct number of cassettes in each run. It also means you should update the software properly whenever you change reagents.

Under default settings the software assigns concentrations “by calculation”. This uses information such as the retort fill level, the number of cassettes processed, the carryover setting and the reagent groups involved to calculate concentration in each station.

Concentrations can also be assigned “by cycles” or “by position” (i.e. by station). These methods rank station concentration by the number of processing runs each station has been used for or the physical order of the stations, respectively.

Leica Microsystems does not recommend the “by cycles” or “by position” options, which must be set by a technical support representative.

For consistently high quality processing always replace reagents as soon as you are prompted, with fresh reagent at the default concentration. If you remove a bottle from the instrument, always check that you enter the correct reagent information for the bottle when you return it. Supervisors

can manually change station concentration values in the Reagent stations screen if they believe

the value there is incorrect. Be sure that you independently verify the concentration if making such a change.

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5.1.3 Thresholds

Each reagent type has a range of thresholds that supervisors can configure on the Reagent types

screen. The thresholds for the pre-defined reagent types should be adequate for most laboratories, but alternative settings may suit some laboratories better – contact customer support for advice before changing threshold settings. Validate any threshold changes using the procedures that apply to your laboratory.

The thresholds fall into two categories:

 Purity thresholds set usage limits for reagents according to their purity

 Temperature thresholds set limits on the retort temperatures for reagents to help ensure high

processing quality and safety.

Purity Thresholds

Peloris uses purity thresholds to limit the use of reagent as it becomes increasingly contaminated with reagent carried over from other groups.

When a threshold is exceeded the software warns you that you need to replace reagent. Under default settings you are able to use a station with out-of-threshold reagent for one more run after such a warning. Following this the station is locked (meaning it cannot be used at all), and/or you cannot run further protocols until fresh reagent is loaded. Your customer support representative can change the number of runs allowed after reagent replacement warnings.

Reagent Setup

Reagent purity is assessed using one or more of four different “reagent threshold check” methods:

 Concentration of the reagent

 Number of cassettes processed with the reagent

 Number of processing runs (cycles) the reagent has been used for

 Number of days the reagent has been loaded on the instrument

By default, all of these methods are available for you to configure for individual reagent types. The

Reagent threshold check section of the Reagent management screen shows the methods

enabled for your system (these settings can only be changed by customer support representatives).

The checking methods are configured to monitor two types of purity threshold:

 reagent change thresholds, and

 final reagent thresholds,

explained below.

Reagent Change Thresholds

Reagent change thresholds set the limits for any use of reagent on the Peloris system. Reagent that has exceeded its change threshold should be replaced with fresh reagent immediately.

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Reagent Setup

Stations with reagent that has exceeded its change threshold are shown with a hatched

icon on the Status screen (bottle icon shown at right).

In addition, the system displays a

warning message.

The Peloris system does not use out-of-change-threshold stations unless no other stations are available. If no other stations are available out-of-threshold stations will be used for one run (default setting) before being locked. Locked stations cannot be used at all until the reagent is replaced. The system will not allow you to load protocols that require a locked station.

Final Reagent Thresholds

Final reagent thresholds set limits on reagent purity for use in protocol steps that precede a change to another reagent group (or type, for protocols configured by type), in the next step.

Final reagent thresholds are set higher than change thresholds. This ensures minimum contamination from the preceding reagent group to the subsequent reagent group.

Reagents that have exceeded their final threshold are displayed as usual on the Status screen,

however Peloris displays a warning message. Following the warning you are able to process one run (default setting) that uses reagent that is out of threshold for the final step. After this, you will not be able to load protocols that require the reagent group affected.

When you are warned that reagent has exceeded the final threshold replace the least pure bottle of the reagent type concerned. The bottle that exceeded the final reagent threshold, triggering the warning, will still have reagent with a relatively high concentration. It will still be acceptable for steps in the protocol sequence before the final step, so it is inefficient to replace it.

Temperature Thresholds

There are three temperature thresholds for each reagent type:

 Ambient — the highest allowable temperature for the reagent in the retort at ambient (and

high) pressure

 Vacuum — the highest allowable temperature for the reagent in the retort when the retort is

evacuated

 Safe — the highest temperature at which it is safe to open a retort containing the reagent.

The Peloris software will not allow you to create protocols that put reagents in conditions that exceed their ambient or vacuum temperature thresholds. The software warns you if you perform an action that requires you to open a retort if the retort contains reagent above its safe temperature threshold.

WARNING

Take extreme care if changing reagent temperature thresholds. Raised thresholds can lead to reagents boiling and/or the release of large quantities of fumes that can overload the filtering system. Boiling reagents can produce excessive pressures within the instrument increasing the chance of reagent contamination and spills.

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5.1.4 Recommended Reagents

While each laboratory is responsible for its choice of reagents and wax, using reagents other than those recommended for Peloris can result in poor processing or compromise instrument reliability. Compliance with the following guidelines will ensure superior tissue processing.

The use of alternative reagents must be validated by the end user according to their local or regional accreditation requirements.

Adequate fixation of tissue samples is required for optimum results and should be achieved prior to placement on Peloris or incorporated into the fixative step of the protocol. The following reagents have been validated for use on Peloris.

Fixatives

 10% Neutral Buffered Formalin (NBF)

Alcohols

 Histological grade ethanol

 Reagent (grade) ethanol

Reagent Setup

 Absolute ethanol

 Isopropyl alcohol (dehydrant)

Denatured ethanol is acceptable if:

 It is at least 99% ethanol, and

 It is denatured with methanol and/or isopropyl alcohol (IPA)

 Ethanol containing acetone must not be used.

Clearing Agents

 Xylene is the recommended clearing agent.

 Xylene-free processing requires the use of isopropyl alcohol as the clearing agent. It has been

fully tested and validated.

Paraffin

 Use histological wax for histology

 Parablocks™

 Paraplast®

Cleaning Agents

 Use ethanol for the cleaning alcohol solution.

 In xylene processing mode, we recommend xylene as the cleaning solvent.

 For true xylene-free processing, we recommend Waxsol™ as the cleaning solvent.

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5.1.5 Tissue Marking

Some laboratories have traditionally added eosin (or other dyes) to formalin or alcohol during tissue processing, to aid in the visualization of tissue during embedding. This practise is NOT recommended for the Peloris tissue processor. The dyes can build up on the liquid level sensors and compromise performance. If you need to mark tissue for embedding, Leica Microsystems recommends you add the dye at the grossing stage.

In spite of this recommendation, eosin can be used on the Peloris if the customer feels there are strong reasons for doing so, and due care is taken. If using eosin on the Peloris add the dye to the fixative in preference to the alcohol. However, rapid turnaround times can mean that tissue is at the grossing stage for only a short time, and fixation steps on the Peloris can also be short. So some customers prefer to add eosin at the alcohol stage. This is also acceptable if due care is taken.

Recommended eosin concentrations for the different stages are given below. Testing was conducted using Surgipath Alcoholic Eosin (1%) – catalog no. 3801600.

CAUTION

If adding eosin to reagents on the Peloris be sure to clean the retorts daily to avoid buildup of dye on the liquid level sensors, which can compromise performance. See Clean Retorts in 7.2 Daily Tasks.

Reagent Setup

Preference 1 – At Grossing

Use 10 mL of 1% liquid eosin per liter of formalin.

You can vary the concentration to correspond with the length of the processing protocol, where some dye will be lost. A disadvantage of staining at grossing is that specimens are not immersed in dyed formalin for the same amount of time.

Preference 2 – In Fixative on Peloris

Use 50 mL of 1% liquid eosin per 5 L Peloris reagent bottle of formalin.

Preference 3 – In Alcohol on Peloris (Xylene)

Use 10 mL to 25 mL of 1% liquid eosin per 5 L Peloris reagent bottle of ethanol (there are eight ethanol bottles in the recommended bottle configuration for xylene processing).

Specimens are immersed in the marking reagent for the same amount of time, giving consistent staining. Protocols longer than two hours may cause overstaining – reduce the eosin concentration as required.

Preference 3 – In Alcohol on Peloris (Xylene-free)

Use 250 mL of 1% liquid eosin per 5 L Peloris reagent bottle of 85% ethanol (there are three bottles of 85% ethanol in the recommended bottle configuration for xylene-free processing).

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5.1.6 Reagent Compatibility

As tissue processing requires the use of incompatible reagents, the Peloris tissue processor software uses a set of rules to ensure that only compatible reagents are allowed to mix. Reagent

mixing usually occurs when a reagent enters a retort of state Empty, containing residual amounts

of the previous reagent. This may happen as part of a protocol, during manual operations or during remote and fill/drain procedures.

The software will not allow you to create a protocol that has an incompatible reagent sequence and you are also prevented from mixing incompatible reagents during remote fill/drain procedures. You cannot run a protocol where the first reagent is incompatible with the retort residue. You can however load a protocol with an incompatible first step but the reagent sequence must be edited during scheduling to select a new first step that is compatible with the retort residue (see Editing the Protocol for a Single Run).

Reagent compatibility varies depending on the action or protocol being undertaken. Use the reagent tables in protocols, conducting manual operations or initiating remote fill/drain procedures.

8.5 Reagent Compatibility Tables to check reagent compatibility before creating

Reagent Setup

3.4.2

5.2 Managing Reagent Types

The Peloris software uses two lists of reagent types – an “active” list for reagents you use and a “dormant” list with all reagent types configured in the system. Supervisors can edit the default concentrations and purity and temperature thresholds (see They can easily move reagents on and off the active list, and create new reagent types. Operators can only view the active list.

See sections below for editing and managing reagent types:

 5.2.1 Pre-defined Reagents

 5.2.2 Editing Active Reagent Types

 5.2.3 Managing the Reagent Types Lists

5.2.1 Pre-defined Reagents

A number of reagent types are pre-defined in the Peloris system. You can edit the properties of these reagent types but they can cannot be deleted. There is no requirement to use the pre-defined types however – you can leave them on the dormant list.

If you change the properties of pre-defined reagent types you cannot use the software to automatically return them to their original values. However the default values for many of the predefined reagents are shown in

8.1 Reagent Threshold Guidelines.

5.1.3 Thresholds) for active reagents.

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5.2.2 Editing Active Reagent Types

List of active reagent

types

Purity thresholds and Temperature thresholds buttons to switch views

Selected reagent type:

select by tapping in the

name cell

Defaults/Concentration:

tap cells to change

Add reagent button: bring dormant reagent onto the active list

Remove reagent button: remove selected reagent from the active to the dormant list

Reagent change thresholds: 

tap cells to change

Final reagent thresholds: tap cells

to change

Use the Reagent types screen (Reagents menu, Types) to view and edit the active reagent

types list. You also access other reagent type management options from this screen.

When you open the screen you see the list of active reagent types. These reagent types are available to set for reagent stations. There are two views of the active list – one each for purity and

temperature thresholds (both views show default concentrations). Change views with the Purity thresholds and Temperature thresholds buttons.

Reagent Setup

Figure 44 and Figure 45 show the two views.

Figure 44. Reagent types screen, purity thresholds view, using recommended reagent types

for xylene-free processing

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Reagent Setup

List of active reagent

types

Purity thresholds and Temperature thresholds buttons to switch views

Selected reagent type

Add reagent button: bring dormant reagent onto the active list

Remove reagent button: remove selected reagent from the active to the dormant list

Max. temperatures: tap cells to change

Defaults/Concentration:

tap cells to change

Figure 45. Reagent types screen, temperature thresholds view, using recommended reagent types

for xylene-free processing

Supervisors can edit the default concentration, purity thresholds, and temperature thresholds for all active reagent types.

You edit a type’s attributes by tapping the appropriate table cell then entering the required value using the resultant keypad. The attributes update immediately and are applied to all reagent stations and protocols that use the reagent type. The changes will not affect running protocols.

Lowering temperature thresholds may make protocol steps invalid. You must lower the step temperature to comply with the new reagent threshold before you can load or run the protocol.

Leica Microsystems does not recommend you lower reagent concentration thresholds. Raising thresholds can help to correct poor quality processing due to impure reagents.

If you no longer use a reagent in the active list you can remove it to the dormant list, to keep the active list as small and easy to manage as possible. Select the reagent type by tapping in its name

cell, then tap Remove reagent.

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5.2.3 Managing the Reagent Types Lists

Selected reagent type:

tap button to select

Reagent group filters: tap to show just the reagent types (in the left of the dialog box) in the selected groups

Complete list of reagent types filtered by reagent group (with buttons at right)

Create reagent: create a new reagent to add to the dormant list

Delete: Delete the selected reagent type (user defined protocols only)

Add reagent: transfer the selected reagent type from the dormant to the active list

Apart from editing the properties of active reagents and moving them to the dormant list, all

management of the reagent types lists uses the Add reagents dialog box ( the Reagent types screen. The dialog box lists all reagent types, ordered by reagent group, on

the left. Filter the list by reagent group with buttons on the right.

Reagent Setup

Figure 46) opened from

To add reagent types to the active list select a reagent type from the list and tap the Add reagent

button.

To add a new reagent type to the dormant list tap the Create reagent button. Choose a reagent

group for the new reagent type and then set a unique name for it.

Use the Delete button to remove user defined reagent types from the dormant list. This deletes

them from the software completely. You cannot delete pre-defined reagent types.

Figure 46. Add reagent dialog box

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5.3 Managing Reagent Stations

The Peloris processor has 20 stations – 16 reagent bottles and four wax chambers.

You must set the stations in the software to the reagent types loaded on the instrument. Once this is done the system tracks each station’s use history (the numbers of runs and cassettes processed and number of days loaded on the instrument), current concentration, and, for wax chambers, the current temperature. See

Supervisors can set the reagent type for each station and change concentration values if they know that actual concentrations are different from those in the system. Both supervisors and operators can change station states if required. The use history details can only be viewed.

It is essential for safe operation of the Peloris that there are bottles loaded into all bays in the

reagent cabinet. If you do not wish to use a particular station, set its state to Dry and (for non wax

stations) insert an empty bottle into the station’s reagent cabinet location.

The choice of which reagent types to load on the instrument, and how many bottles of each, is an important question that you must decide along with consideration of the protocols you run. See Station Configurations for configurations suitable for the default protocols.

Stations in 5.1.1 Reagent Groups, Types and Stations for further details.

Reagent Setup

8.3

5.3.1 Reagent Stations Screen

Use the Reagent stations screen (Reagents menu, Stations) to set up and manage reagent

stations. There are two views of the screen – one for the 16 reagent bottles and the other for the

four wax chambers. Change views with the Reagent bottles and Wax chambers buttons.

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Reagent Setup

Reagent bottles and Wax chambers

buttons to switch views

Selected station: tap in

Station cell to select

Hatched cell indicates

change threshold

exceeded. Out-of-

threshold

concentration value

shown in red

Since changed: the use history of each station – view only

Station: station

number with reagent

group color code

Type: reagent type in

station. Tap cell to

change

Conc.: current concentration of reagent in station. Tap cell to change

State: current state of station. Tap cell to change

Reagent bottles and Wax chambers

buttons to switch views

Selected station: tap in

Station cell to select

Hatched cell indicates

change threshold

exceeded. Out-of-

threshold

concentration value

shown in red

Since changed: the use history of each station – view only

Station: station

number with reagent

group color code

Type: reagent type in

station. Tap cell to

change

Conc.: current concentration of reagent in station. Tap cell to change

State: current state of station. Tap cell to change

Temp.: current temperature in the wax chamber

See Figure 47 and Figure 48 for descriptions of the information and options on the Reagent stations screen.

Figure 47. Reagent stations screen, reagent bottles view

Figure 48. Reagent stations screen, wax chambers view

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5.3.2 Setting Reagent Station Properties

See sections:

 Assigning New Reagents to Stations

 Changing Reagent Concentration

 Setting Station States

CAUTION

Altering reagent station configurations while protocols are running may cause abandoned protocols.

Assigning New Reagents to Stations

If you change the type of reagent loaded in a station you must change the reagent type assigned to the station in the software.

Follow the steps below to change the reagent type for a station:

Reagent Setup

1. Remove the bottle (or drain the wax chamber) with the reagent type you are replacing.

2. In the Reagent stations screen tap in the station’s Type cell to open the Reagent selection dialog box.

3. Select the new reagent type from the list.

The dialog box shows all the current active reagent types (see 5.2.3 Managing the Reagent Type s Li s ts).

4. When prompted, tap Yes to reset the station properties. This sets the use history counts to

zero and the station concentration to the default for the new reagent type.

5. Clean the bottle if necessary and fill with fresh reagent of the new type. Load the bottle back onto the instrument (or fill the wax chamber).

6. For a bottle, in the Inserted bottle configuration dialog box, select the bottle in the table and then tap the Emptied and refilled button.

For a wax chamber, set the station state to Full on the Reagent stations screen.

When you change the reagent type for a station on the Reagent stations screen you are always prompted to reset the station’s concentration and use history. If you select No you will retain the

previous reagent’s concentration and use history. Use this option only if you are correcting a previous error in the identification of the reagent in the station, and you are not actually changing the station’s contents.

WARNING

Always ensure that the reagents configured in the software are the actual reagents loaded on the instrument. A station containing different reagent could damage tissue samples.

Page 87

Reagent Setup

Changing Reagent Concentration

You can set a station’s “calculated” concentration value. Tap the station’s Conc. cell. Enter the new

concentration in the keypad.

WARNING

Setting Station States

All users can change station states (Full, Empty, In use, Dry, and Not molten) in the Reagent stations screen.

For reagent bottles you should not normally need to do this – you update the bottle states when you remove and replace bottles and then the software tracks the state automatically. Change bottle station states only if the wrong state is displayed or you want to make a full bottle unavailable for

use (by setting it to In use).

For wax chambers you must change the station state in the Reagent stations screen as a normal

part of wax replacement.

To change a station state tap the station’s State cell and select the appropriate icon in the dialog

box.

Figure 49. Station state dialog box for reagent stations (L) and wax stations (R)

See 3.3.1 Status Area for detailed information on reagent station states.

WARNING

Ensure you set the station state to the actual condition of the station. An incorrect reagent station state may cause fluid leaks or abandoned processing runs.

Page 88

5.4 Replacing Reagents

Always replace reagents as soon as possible after the system alerts you.

There are two methods to replace reagent in bottles:

 Remote fill/drain — pump the old reagent out and new reagent back in without removing

the bottle, using commands on the Remote fill/drain screen.

 Manually — remove the bottle, drain and refill, then replace on the instrument.

For wax you must drain the chamber using the Remote fill/drain screen, fill the chamber

manually, and then update the software.

See sections below:

 5.4.1 Remote Fill/Drain Screen

 5.4.2 Remote Fill/Drain Connections

 5.4.3 Replacing Reagent – Remote Fill and Drain

 5.4.4 Replacing Reagent – Manual

Reagent Setup

 5.4.5 Replacing Wax

 5.4.6 Filling and Draining Retorts

5.4.1 Remote Fill/Drain Screen

Use the Remote fill/drain screen (Reagents menu, Remote fill/drain) to drain the wax baths

and to fill and drain reagent bottles without removing them from the instrument. You are able to fill/drain stations individually or as a group of compatible stations in a single operation. You can also fill and drain retorts from this screen to enable recovery from partially completed fill/drain operations.

All users can perform the functions on the Remote fill/drain screen.

Page 89

Figure 50 shows the Remote fill/drain screen with the main features described:

Fill to/Drain from bottles, Drain to waste, or Fill/Drain retort:

start fill or drain when appropriate station, remote source and retort are selected

Abandon:

stop the drain or fill

Wax waste:

select with a wax

chamber to drain the

chamber

Remote:

select with a retort and

bottle to fill or drain

the bottle

Retort A: scheduled fill/drain operations for retort A

Retort B: scheduled fill/drain operations for retort A

Wax System: scheduled fill/drain operations for the wax chambers

Figure 50. Remote fill/drain screen

Reagent Setup

5.4.2 Remote Fill/Drain Connections

The remote fill/drain line and the wax drain outlet sit above the carbon filter in the reagent cabinet (see

Figure 52). A protective flap covers the outlets. The wax waste line is heated to ensure that

the wax does not solidify during the drain.

 Before draining a wax station, open the upper reagent cabinet door, slide back the fill/drain flap

 Before filling or draining reagent bottles, connect the remote fill/drain hose (see Figure 53) to

Figure 51. Remote fill/drain flap closed Figure 52. Remote fill/drain flap open with reagent

then fit the wax waste hose to the wax waste line (right connection in Ensure the wax waste hose drains into a suitable container.

Ensure the hose remains out of the drained wax so that wax can’t solidify on the end of hose.

the remote fill/drain line (left connection in Figure 53). The hose has a push-fit coupling that ensures a secure connection to the line.

line (left) and wax waste line (right).

Figure 52). 

Page 90

Reagent Setup

To fit the hose, open the upper reagent cabinet door, slide back the fill/drain flap, and push the coupling onto the end of the line. To remove the hose, slide back the locking ring (item 1 in Figure 53) and pull the hose off the remote fill/drain line.

Figure 53. Remote fill/drain hose with locking ring (1)

WARNING

Always ensure that you fill from or drain to a large stable container. The fill/drain functions include a strong purge which may cause an unstable container to tip over and spill. The container must also be of sufficient volume to easily accommodate all of the drained fluid.

If you need to use a small container you must support the container and hose during the fill or drain.

WARNING

Always use the hose supplied with the Peloris system for reagent bottle operations.

WARNING

Ensure you use the correct size wax drain hose to avoid wax leakage. Old and new instruments have different sized wax waste line connectors.

WARNING

Always wear suitable eye protection and other protective clothing when handling reagents to protect yourself from splashed reagent.

Page 91

5.4.3 Replacing Reagent – Remote Fill and Drain

Select the retort to use

Select the bottle or bottles to drain

Select Remote icon

When bottle, retort and

Remote are selected tap Drain from bottle(s) to

start the drain

You can drain and then refill reagent bottles without removing the bottles from the instrument. The process drains each bottle to a retort then drains the retort to the remote fill/drain line. The reverse procedure is used for the fill.

If you routinely use remote drain and fill do not forget to check if bottles need cleaning, once a week.

Before you begin a remote fill or drain ensure there is a retort available:

 the retort must not have a protocol loaded or running;

 The retort must be clean or empty;

 The retort residue (if any) must be compatible with the reagent in the bottle(s).

Follow the instructions below to replace reagent in a bottle.

Drain

1. Connect the remote fill/drain hose and place the end in a suitable container (see 5.4.2 Remote Fill/Drain Connections).

Reagent Setup

2. From the Remote fill/drain screen (Reagents menu, Remote fill/drain), select:

 The retort to use

 The Remote icon

 The bottle(s) to drain (multiple bottles must all have reagent in the same group).

Figure 54. Remote fill/drain setup for draining bottles

3. Tap Drain from bottle(s) to begin the drain.

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Reagent Setup

4. When prompted, check that the retort lid is closed and the remote fill/drain hose is properly connected.

Tap OK to begin the drain.

5. The instrument will now drain the bottle(s) via the selected retort.

Monitor the drain progress in the status panel.

When the drain completes, the retort state will be Empty and the bottle state Dry.

WARNING

Do not remove the remote fill/drain hose until the software indicates the process is complete and pressurized air has cleared the hose. A cessation of reagent flow is not an indication that the procedure is complete.

Fill

6. Place the hose into the container of fresh reagent.

The reagent source must be above 5 °C to ensure that all reagent sensors operate correctly.

7. F r o m t h e Remote fill/drain screen, select:

 The retort to use

 The Remote icon  The bottle(s) to fill (multiple bottles must all be Dry and set to the same reagent type)

Any bottle residue must be compatible with the new reagent.

8. Tap Fill to bottle(s) to begin filling.

9. When prompted, check that the retort lid is closed and the remote fill/drain hose is properly connected.

Tap OK to begin the fill.

10. The Remote fill/drain - Reagent details dialog box will now appear.

Figure 55. Reagent details dialog box with reagent type, concentration and

use history for the new reagent

11. Confirm that the reagent type, concentration and use history details are correct, or tap in the table cells for any of these values to change the settings.

If you set a new reagent type the station must have already been set to that type (see Assigning New Reagents to Stations in 5.3 Managing Reagent Stations). The reagent must be compatible with the retort and bottle residue.

Tap OK to start the fill.

Page 93

Reagent Setup

12. The instrument will now fill the bottle(s) via the selected retort.

The fill volume is determined by the reagent fill level set in the Instrument settings screen

(see

6.2.1 Instrument Settings).

Monitor the fill progress in the status panel.

When finished the retort will have an Empty state and the bottle will have a Full state.

At any time during the drain or fill you can tap the Abandon button to terminate all current and

pending fill/drain operations.

If you abandon a drain such that both the retort and bottle are left partially full, you must drain the

retort back to the original bottle to continue. To drain the retort, deselect the Remote icon then tap the Drain retort button.

WARNING

Do not open a retort while it is being used for a remote fill or drain operation as the retort could be pressurized and may contain hot reagent and fumes. Allow the fill or drain to complete or abandon the process before opening the retort.

Remote Fill and Drain Sequences

The following reagent sequences are recommended when filling and draining multiple bottles:

Order Drain sequence Fill sequence

1 Fixatives Cleaning solvents

2 Cleaning alcohols Clearers

3 Dehydrants Defatting solvents

4 Defatting alcohols Defatting alcohols

5 Defatting solvents Cleaning alcohols

6 Cleaning solvents Dehydrants

7 Clearers Fixatives

Page 94

5.4.4 Replacing Reagent – Manual

Tap in the table row to

select the bottle, then

select an option button

below

No change:

select if you did not do

anything to the

reagent in the bottle

Topped off/up:

select if you added a

small amount of reagent

to the bottle to bring up

its level

Changed: select ONLY if you replaced the bottle contents with fresh reagent

To replace bottles manually remove the bottles and dispose of the old reagent following your laboratory’s standard procedures. Clean the bottle if necessary, and then fill with fresh reagent. Load back on to the instrument.

When the bottle is reinserted the Inserted bottle configuration dialog box opens, showing the

reagent type, concentration and use history for either:

 the bottle when it was removed, or

 the bottle as configured in the Reagent stations screen, if you assigned a new reagent type

to the station after the bottle was removed (see

Reagent Setup

Assigning New Reagents to Stations).

Figure 56. Inserted bottle configuration dialog box

The bottle state is set to Unknown in the dialog box.

Tap the table row and select one of the options at the bottom of the dialog box:

 Changed — select if you replaced the old reagent with fresh reagent.

With this option the software prompts you to accept the default concentration for the reagent in the station. If you know the concentration to be other than the default you can enter a different concentration.

The use history values are all set to zero.

If you changed the reagent type in the bottle you cannot update it in the software from this

dialog box. Tap No change and then remove the bottle again. Change the reagent assigned to the bottle in the Reagent stations screen (see

Assigning New Reagents to Stations), then

reinsert the bottle.

 Topped off/up — select if you did not change all the reagent but added a small amount of

fresh reagent of the same type to bring up its level in the bottle.

With this option the bottle state changes to Full. The concentration and use history details do

not change.

 No change — select if you made no changes to the reagent in the bottle at all.

Page 95

With this option you must select the bottle state. The concentration and use history details do not change.

WARNING

Ensure lids are tight and the bottles are correctly plugged into the manifold after replacing reagent to avoid reagent spills.

5.4.5 Replacing Wax

To re pl a ce w ax :

1. drain the wax chamber using the Remote fill/drain screen commands,

2. refill the wax chamber manually with molten or solid wax, and then

Reagent Setup

3. reset the state of the wax chamber.

Before you begin ensure there is a retort available. Draining wax does not fill a retort, but it does use retort scheduling resources, so at least one retort must be available. The retort does not need to be clean.

The wax to be drained must be molten.

Follow the instructions below to replace wax in a chamber.

Page 96

Reagent Setup

Select the wax chamber or chambers to drain

Select Wax waste icon

When wax chamber and Wax

waste icon are selected tap

Drain to waste to start the

drain

Drain

1. Connect the wax waste hose and place the end in a suitable container (see 5.4.2 Remote Fill/ Drain Connections).

2. From the Remote fill/drain screen (Reagents menu, Remote fill/drain), select:

 The wax stations to drain

 The Wax waste icon

Figure 57. Remote fill/drain setup for draining wax chambers

3. Tap Drain to waste to begin the drain.

4. When prompted, check that the wax waste hose is properly connected and feeding into a suitable container.

Tap OK to begin the drain.

5. The instrument will now drain the chamber(s).

Monitor the drain progress in the status panel. Wax drains may take up to three minutes.

When the drain completes, the chamber state will be Empty.

WARNING

The wax leaving the waste wax line will be hot and may cause burns. Make sure the wax drains to a suitable container and stand clear while it drains.

WARNING

Do not remove the wax drain container or hose until the software indicates that the drain has completed. A cessation of wax flow is not an indication that the drain procedure is complete.

If no wax drains it is likely that the wax hose is blocked. If you remove a blocked hose before the drain is abandoned hot wax will spurt from the front of the instrument. Abandon the drain before removing the hose and melting the wax with hot water.

6. To stop wax solidifying in the drain hose, promptly remove the hose from the drained wax.

At any time during the drain you can tap the Abandon button to terminate all current and pending

fill/drain operations.

Page 97

Fill

7. Fill the wax chamber with molten or solid wax.

8. Open the Reagent stations screen, wax chambers view (Reagents menu, Stations, then tap the Wax chambers button).

The row for the drained wax chamber shows the default concentration and all use history

values set to zero. The station state is Dry.

The reagent type is unchanged from the wax that you drained unless you changed the type assigned to the station after the drain (see

9. Tap the State cell for the chamber:

 If using molten wax, set the state to Full.  If using solid wax, set the state to Not molten to begin the rapid wax heating process.

While in the Not molten state the wax bath chamber temperature is higher than normal

to ensure the wax melts quickly.

You may need to add extra wax as it melts.

The station’s state automatically changes to Full when the wax is ready to use.

5.4.6 Filling and Draining Retorts

Reagent Setup

Assigning New Reagents to Stations)

The Remote fill/drain screen allows you to fill and drain the retorts to assist recovery from

incomplete remote fill/drain operations. The retort fill and drain functions operate with a series of rules designed to avoid reagent contamination, reagent overflow spills and reagent overheating. You can override some rules but this will often result in reduced reagent concentration.

You can also fill and drain retorts using the Manual operations screen (see 6.1.1 Manual

Operations).

The rules for manually filling and draining retorts are as follows.

 The retort must be clean or empty before you commence a retort fill operation.

 If the retort is empty the selected station must have compatible reagent (see 8.5 Reagent

Compatibility Tables).

 You cannot fill a retort with a reagent that has a temperature threshold below the set retort

temperature.

 When draining a retort, the reagent must return to its original station.

 When draining a retort, the station must have sufficient capacity for the retort contents.

To avoid fluid spills, ensure adequate station capacity before overriding insufficient capacity errors.

To fill or drain a retort select the retort and the reagent station to fill from or drain to, on the

Remote fill/drain screen. Tap the Fill retort or Drain retort button. To stop the fill at any stage, tap the Abandon button.

WARNING

Never fill a reagent station when its contents are in a retort. This may cause fluid spills.

Page 98

Settings & Ancillary Operations

This chapter describes basic system configuration options and ancillary operations such as manually pressurizing a retort or heating a wax line, viewing the event log, handling alarms, changing user access level, and transferring system files onto external media.

Access reagent-related ancillary options from the Reagents menu:

 6.1.1 Manual Operations

 6.1.2 Reagent Management

All other ancillary functions are in the Control menu:

 6.2.1 Instrument Settings

 6.2.2 Device Settings

 6.2.3 Service Settings

 6.2.4 Event Log

 6.2.5 Alarms

 6.2.6 Access Level

 6.2.7 File Transfer

6.1 Reagents Menu

Manually control reagent handling components of the instrument or configure or view basic

reagents settings in two screens opened from the Reagents menu:

 6.1.1 Manual Operations

 6.1.2 Reagent Management

Page 99

6.1.1 Manual Operations

Fill/Drain retort:

fill or drain the retort

from or to the selected

station

Stirrer: set the retort

stirrer to high, medium

or low speed, or off

Temp.:

set the retort

temperature

Retort A controls

Wax heater: turn on/off heaters for wax path

Pressure: set the pressure in the retort – ambient, vacuum, pressure, or pressure/vacuum cycle

Abandon: stop a fill or drain operation

Retort B controls

Vent wax:

release pressure or

vacuum in wax chambers

The Manual operations screen (Reagents menu, Manual operations) allows you to manually

control the instrument. The screen displays the current instrument status including station states, the retort states and the retort condition. You control the instrument by selecting instrument elements from the status area and control functions from the panels on either side.

All users can perform manual operations functions.

You can fill a retort from any station and then set conditions in the retort: temperature, pressure and stirrer. If intending to move wax into a retort preheat the wax path by turning on the wax heater. Use the wax vent function to neutralize the pressure in the wax bath so the wax bath lids can be opened easily and safely.

You cannot override a running protocol from the Manual operations screen and you cannot fill or

drain a retort that has a loaded protocol.

Figure 58 shows the Manual operations screen with function buttons explained:

Settings & Ancillary Operations

Figure 58. Manual operations screen

Retort Temperature Range

The retort temperature range is limited to the following values.

 Reagent — 35 ºC minimum to 85 ºC maximum (restricted to 65 ºC maximum when running

tissue processing protocols).

 Wax — (Wax melting point + 2 ºC) minimum to 85 ºC maximum (restricted to 77 ºC when

running standard protocols).

View the current wax melting point temperature on the Reagent management screen.

Page 100

Settings & Ancillary Operations

Additional limitations may apply depending on the retort state and the reagent in the retort. You cannot raise the retort temperature above the safe temperature threshold of the reagent.

Wax Transfers

The wax path (comprising the wax valves and the transfer pipes) and the retort must be at the wax

standby temperature before you attempt to fill a retort with wax. Use the Wax heater buttons for at least five minutes to enable wax path heating. Use the Temp. button to set the retort to the wax

standby temperature and wait until the retort reaches the temperature before filling.

Filling and Draining Retorts

Fill or drain the retorts from any reagent station using commands on the Manual operations

screen. The fill and drain functions operate with a series of rules designed to avoid reagent contamination, reagent overflow spills and reagent overheating. You can override some rules but this will often result in reduced reagent concentration.

The rules for manually filling and draining retorts are as follows.

 The retort must be clean or empty before you commence a retort fill operation.

 When filling a retort, the selected reagent station must be compatible with the retort residue.

See

8.5 Reagent Compatibility Tables.

 You cannot fill a retort with a reagent that has a temperature threshold below the set retort

temperature.

 When draining a retort, the reagent should return to its original station.

 You cannot drain wax to a reagent bottle or non-wax reagents to a wax station.

 When draining a retort, the station must have sufficient capacity for the retort contents.

Always ensure the retort is in a suitable state before filling. To fill, select the retort and reagent

station then tap Fill retort.

To drain a retort select the retort and the station the retort contents came from. Tap the Drain retort button. The system will not allow you to drain a retort to a station other than the one the

reagent came from.

You can stop a fill or drain at any time with the Abandon button. Recover from an abandoned fill

or drain by restarting the operation, or return the reagent to the station or retort it came from with the opposite operation.

WARNING

Do not open a retort if it has been filled with hot reagent and pressurized using the manual operations functions. Always use the manual operations functions to de-pressurize a retort before opening and wear suitable protective clothing (including eye protection) if the retort contains hot reagent.

Leica PELORIS, PELORIS II User Manual

Specifications and Main Features

Frequently Asked Questions

User Manual

Legal Notices

Contacting Leica Microsystems

Software Licence Terms

Safety Notices

Regulatory Approvals

Contents

Introduction

1.1 Summary of Chapters

1.2 Using the Software

1.2.1 Basic Operation

1.2.2 Navigation

1.2.3 Access Levels

1.3 Help

Hardware

 2.1 Switching On and Shutting Down

2.2 Retorts

 2.2.1 Opening and Closing Retort Lids

2.2.2 Fill Levels

2.2.3 Magnetic Stirrer

2.2.4 Cassette Baskets

2.3 Wax Bath

2.4 Reagent Cabinet

2.4.1 Reagent Bottles

2.4.2 Condensate Bottle

2.4.3 Carbon Filter

2.5 Touch-screen

2.6 External Vapor Removal Systems

2.7 Alarm Connections

Running Protocols

 3.1 Quick Start – Running a Protocol

3.2 Cleaning Protocols

3.3 Status Screen

3.3.1 Status Area

3.3.2 Protocol Panels

3.4 Protocol Run Options

 3.4.1 Scheduling Protocols

3.4.2 Editing the Protocol for a Single Run

3.5 Pausing and Abandoning Protocols

3.6 Retort Scheduling

3.6.1 Delayed End Times and Initial Fills

3.6.2 Unavoidable Reagent Clashes

3.6.3 Unavailable Reagents

Protocol Setup

 4.1 Protocol Overview

 4.1.1 Protocol Types

4.1.2 Reagent Selection Method

4.1.3 Pre-defined Protocols

4.1.4 Protocol Validation

4.1.5 Carryover Setting

4.1.6 Saving Protocol Files

4.2 Creating, Editing and Viewing Protocols

 4.2.1 The Protocol Selection Screen

4.2.2 Editing Protocols

4.2.3 Creating New Protocols

4.2.4 Viewing Protocols

Reagent Setup

 5.1 Reagents Overview

5.1.1 Reagent Groups, Types and Stations

5.1.2 Concentration Management

5.1.3 Thresholds

5.1.4 Recommended Reagents

5.1.5 Tissue Marking

5.1.6 Reagent Compatibility

5.2 Managing Reagent Types

 5.2.1 Pre-defined Reagents

5.2.2 Editing Active Reagent Types

5.2.3 Managing the Reagent Types Lists

5.3 Managing Reagent Stations

5.3.1 Reagent Stations Screen

5.3.2 Setting Reagent Station Properties

5.4 Replacing Reagents

 5.4.1 Remote Fill/Drain Screen

5.4.2 Remote Fill/Drain Connections

5.4.3 Replacing Reagent – Remote Fill and Drain

5.4.4 Replacing Reagent – Manual

5.4.5 Replacing Wax