UVP ColonyDoc-It Imaging Station User Manual

ColonyDoc-It™ Imaging Station

Instruction Manual

UVP, LLC Ultra-Violet Products Ltd.

2066 W 11th Street, Upland, CA 91786 Unit 1, Trinity Hall Farm Estate
Tel: [phone] Nuffield Road, Cambridge CB4 1TG UK
Fax: [phone] Tel: [phone] / Fax: [phone]
Email: [e-mail] Email: [e-mail]

Web site: uvp.com

81-0294-01 Rev. E

ColonyDoc-It Imaging Station 2

ColonyDoc-It Imaging Station 3

END USER LICENSE AGREEMENT

PLEASE READ THE FOLLOWING AGREEMENT CAREFULLY

This Agreement is between UVP, LLC of 2066 West 11th Street, Upland, California 91786 (hereinafter “Licensor”) and the
end user of UVP software (hereinafter “Licensee”).

Licensor has developed and offers to Licensee on a non-exclusive basis pursuant to the terms and conditions set forth
hereinafter, the following software, including related copyrighted instructional materials, (collectively referred to hereafter as
“The Software”):

DOC-IT COLONY SOFTWARE

The terms of this Agreement apply without regard for the method by which the Software is acquired by Licensee. While the
most common medium for acquiring the Software from Licensor is by CD-ROM, the Software may, in some instances, be
acquired by download; from a Licensor thumb drive acquired from Licensor; from a CD ROM acquired from Licensor from a
network location; or may be pre-installed on the Licensee‟s computer.

By using the Software, you are agreeing to be bound by all terms of this License. If you do not agree to the terms of the
License, you are not authorized to use the Software in any manner.

LICENSE

In consideration of payment of the License fee, which is a portion of the price you paid, the software, including any images
incorporated in or generated by the software, and data accompanying this License and related documentation are licensed
(not sold) to you by Licensor. Licensor does not transfer title to the Software to you; this License shall not be considered a
“sale” of the software and Licensor retains full and complete title to the Software and all intellectual and industrial property
rights therein. It is to be understood that this non-exclusive and personal License only gives you the right to use and display
the software. You must treat the software like any other copyrighted material. You may not copy the Software or the written
material accompanying the software without the express written consent of Licensor.

RESTRICTIONS

The Software contains copyrighted materials, trade secrets, and other proprietary material. You may not re-sell, decompile,
reverse engineer, disassemble or otherwise reduce the Software to a human-perceivable form. Except as provided for in
this License, you may not copy, modify, network, rent, lease, or otherwise distribute the Software; nor can you make the
Software available by “bulletin boards”, on-line services, remote dial-in, or network or telecommunications links of any kind;
nor can you create derivative works or any other works that are based upon or derived from the Software in whole or in part.
You may not transfer the license rights to the Software to another party.

TERMINATION

This License is effective until terminated by either party. You may terminate this License at any time by returning the
Software to Licensor or destroying any permanent form of the software and all related documentation and all copies and
installations thereof, whether made under the terms of this License or otherwise. This License will terminate immediately
without notice from Licensor if you fail to comply with any provision of this License. Upon termination, you must destroy or
return to Licensor any permanent form of the software and related documentation.

LIMITED WARRANTY AND DISCLAIMER

Licensor warrants the software and related documentation to be free from defects in materials and workmanship, under
normal use for a period of ninety (90) days from the date of purchase as evidenced by a copy of the sales receipt or packing
slip. Licensor‟s entire liability and licensee‟s exclusive remedy will be replacement of the defective software and related
documentation or refund of the purchase price (at licensor‟s election) upon return of the software and related documentation
to licensor with a copy of proof of purchase. This warranty gives you specific legal rights and you may also have other rights
which vary from jurisdiction to jurisdiction. You expressly acknowledge and agree that use of the software is at your sole risk
after the ninety (90) days. The software and related documentation are provided without warranties and/or conditions of any
kind either express or implied, except as provided above. Licensor expressly disclaims all other warranties and/or
conditions, express or implied, with respect to software and related documentation including, but not limited to, the implied
warranties and/or conditions of merchantability and fitness for a particular purpose. Licensor does not warrant that the
functions contained in the software will be uninterrupted or error-free, or that defects in the software will be corrected after
the ninety (90) days. Furthermore, after the ninety (90) days, licensor does not warrant or make any representation
regarding the use or the results of the use of the software and related documentation in terms of their correctness, accuracy,
reliability, or otherwise. The limitations of liabilities described in this section also apply to the third party suppliers of
materials used in the software. No oral or written information or advice by licensor or by representatives of licensor shall

ColonyDoc-It Imaging Station 4

create warranties, and/or conditions, or in any way increase the scope of this limited warranty. Licensee assumes the entire
cost of all necessary servicing, repair or correction after the ninety (90) days. Some jurisdictions do not allow the exclusion
of implied warranties, so the above exclusion may not apply to you.

LIMITATION OF LIABILITY

Under no circumstances, including negligence, shall licensor be liable for any special or consequential damages that result
from the use of, or the inability to use, the software or related documentation, even if licensor or authorized representative of
licensor has been advised of the possibility of such damages. Some jurisdictions do not allow the limitation or exclusion or
liability or consequential damages, so the above limitations or exclusion may not apply to you. In no event shall licensor‟s
total liability to you for all damages, losses, and causes of action (whether in contract, tort (including negligence) or
otherwise) exceed the amount paid by you for the software.

INTENDED USE

If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may be
impaired.

GOVERNING LAW AND SEVERABILITY

This License shall be governed by and construed in accordance with the laws of the State of California, without giving effect
to any principles of conflicts of law. Any actions, suits or proceedings instituted in connection with this License, the Software
and/or related documentation shall be instituted and maintained exclusively in the Superior Court for the State of California,
County of Los Angeles, or in the United States District Court for the Central District of California. By entering this License
you hereby consent to the venue and jurisdiction of the aforesaid courts. If any provision of this license shall be unlawful,
void, or for any reason unenforceable, then that provision shall be deemed severable from this License and shall not affect
the validity and enforceability of any remaining provision. This is the entire agreement between the parties relating to the
subject matter herein and shall not be modified except in writing, signed by both parties.

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Table of Contents

Introduction ............................................................................................................................................................................... 7

Components ............................................................................................................................................................................. 7

System Requirements............................................................................................................................................................... 8

System Specifications ............................................................................................................................................................... 8

Installing the ColonyDoc-It ........................................................................................................................................................ 9

Installing the Hardware ............................................................................................................................................... 9

Installing the Software .............................................................................................................................................. 11

Registering the Software .......................................................................................................................................... 11

Counting Colonies .................................................................................................................................................................. 13

Quick Capture ........................................................................................................................................................... 13

Automatic Counting .................................................................................................................................................. 15

Manual Counting ...................................................................................................................................................... 16

Creating Templates .................................................................................................................................................. 20

User Defined Template Counting ............................................................................................................................. 21

Fluorescent Colony Counting ................................................................................................................................... 22

Zone Analysis ........................................................................................................................................................... 24

Renumbering Colony/Zone Values ........................................................................................................................... 28

Spiral Plate Counting ................................................................................................................................................ 29

Editing Colonies ...................................................................................................................................................................... 31

Add Colonies ............................................................................................................................................................ 31

Delete Colonies ........................................................................................................................................................ 32

Manual Split Colonies ............................................................................................................................................... 33

Auto Split Colonies ................................................................................................................................................... 34

Merging Colonies ...................................................................................................................................................... 35

Using the Software ................................................................................................................................................................. 36

Changing Filter Settings ........................................................................................................................................... 36

Preferences .............................................................................................................................................................. 37

Toolbars ................................................................................................................................................................... 39

Reporting Functions ................................................................................................................................................................ 40

Classes ..................................................................................................................................................................... 40

Colonies ................................................................................................................................................................... 41

Statistics ................................................................................................................................................................... 41

Distribution................................................................................................................................................................ 42

Exporting to Excel ..................................................................................................................................................... 42

Supporting 21 CFR Part-11 Compliance................................................................................................................................. 44

Purpose .................................................................................................................................................................... 44

Features ................................................................................................................................................................... 44

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Usage ....................................................................................................................................................................... 44

Servicing the ColonyDoc-It ..................................................................................................................................................... 45

Cleaning and Care .................................................................................................................................................... 45

Replacing Switches .................................................................................................................................................. 46

Replacing Fuses ....................................................................................................................................................... 46

Ordering Replacement Parts and Accessories ......................................................................................................... 46

Troubleshooting ........................................................................................................................................................ 46

Return Service Procedure ........................................................................................................................................ 47

Technical Support ..................................................................................................................................................... 48

Warranty ................................................................................................................................................................................. 48

ColonyDoc-It Imaging Station 7

 Colony counter

 Black plate

 USB cord

 Power cord

 Software CD

Introduction

This manual covers the installation and user instructions for the ColonyDoc-It Imaging Station.

The innovative, compact design enables users to process automated, fast and accurate colony counting. The high
resolution digital color camera allows users to capture white light and fluorescent marked colonies and a wide array
of samples. The sophisticated yet intuitive system offers researchers easy detection and analysis of media.

The software loads on the user‟s computer for camera control, image capture and colony counting. The software
provides automatic and manual counting capabilities plus user defined templates for speeding up research
experiments. Users can define specific counting parameters including color differentiation and filter identification by
group or size. Once the colonies are counted, the results display on the screen. Images and data can be saved in
multiple formats and the data can be exported to Excel. The software supports 21 CFR Part 11 compliance.

Components

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Electrical ratings:

Model Numbers:

97-0539-01, 97-0539-04

100-115V, 60Hz, 0.25 Amps

Model Numbers:

97-0539-02, 97-0539-05

230V, 50Hz, 0.13 Amps

Operational Ratings:

Unit intended to be used indoors

Altitude must not exceed 2000 m

Operating temperatures not to exceed 0°C to 40°C (32°F to 104°F)

Operating humidity not to exceed 85%

System Requirements

 Operating System: Windows XP Professional with Service Pack-2 (32 bit only), Vista (32 bit only),

Windows 7 (32 bit only)

 Internet Explorer 6.0 or higher (To determine the version of Internet Explorer, open Internet Explorer and

click on Help > About)

 Minimum resolution: 1024 x 768

 Intel Pentium Processor or equivalent, 1.6 GHz or higher

 1GB (2GB recommended) of RAM or greater

 200 MB of available hard disk space for the program, more for data

 To avail the functionality of 21 CFR Part 11, then the partition must be formatted with NTFS.

 CD-ROM drive

System Specifications

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Set the ColonyDoc-It Imaging Station on a
level surface.

Plug in one end of the power cord to the back
of the ColonyDoc-It Imaging Station and the
other end into a power outlet. To maintain
safety at all times, ensure that the unit is not
hard to disconnect at the location chosen.

Turn on the ColonyDoc-It by switching the I/0
switch to I located at the back of the station.

Plug one end of the USB cord to the back of
the ColonyDoc-It and the other end into a USB
port in the computer.

The ColonyDoc-It doors can be removed by
hand-loosening the two thumbnuts on the
inside of each door.

Installing the ColonyDoc-It

Installing the Hardware

Removing the Doors

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Remove the four brass thumbnuts on the
filter box and pull the filter box from the
housing.

Remove the two thumbnuts that hold the filter
frame to the filter box.

 Place the filter over the opening.

 Replace the filter frame and thumbnuts.

 Reinstall the filter box into the unit.

NOTE: It is possible to install a filter when the
filter box is installed in the unit. However,
care must be taken to avoid touching the
shiny sides of the filter.

Installing the Filter

Note: Filters come as an optional accessory so this step is only necessary if an optical filter will be used with the
system.

The filter trays are located in the filter box attached to the ceiling of the unit. To access the trays:

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The InstallShield Wizard window will
appear.

Follow the instructions for installation.

Once installation is complete, refer to the

Registering the Software in this manual to

activate the software.

Double click the software icon on the
desktop.

To activate the software, registration is
required. To immediately activate the
software through the internet, choose On
the fly activation. If the computer is not
connected to the internet, please follow the
instructions for Offline activation or call
UVP to register the software.

Click Next to continue.

Installing the Software

Insert the Doc-It Colony Counter CD into the CD drive in the computer.

Registering the Software

Opening the Software

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Complete all required information on the
form.

Fill out the Serial Number located on the
CD. The number should be four sets of six
numbers.

Click onto Get Activation No. and then
click onto Activate when the Activation

Number appears in the box.

Already have an activation ID is useful

when reloading the software after receiving
an initial activation code.

If the computer is not connected to the
internet, click Offline activation to register
the software. This allows the user to obtain
the activation code and enter it at another
time.

Click Next to continue.

Click the link provided and complete the
form to obtain instructions. Click Finish.

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Ensure that the Camera Control module is active. See the image of the screen below noted by the green circle.
The text must be black as shown. If the Camera Control is inactive (with grey text) proceed to the troubleshooting

section: Inactive Camera Window.

Select the Petri dish plate diameter from the Camera Control module. The choices are 6cm, 10cm, and 15cm.

Select the smallest colony size for this plate. The choices are <1mm and 1mm+. If <1mm is selected the
smallest colony size is below 1mm. The count will be faster if 1mm+ is chosen.

Choose the White Light option from Colony Lighting. The Dim to Bright slider will be disabled unless using the

Fluorescent Colony Lighting option. If counting fluorescent colonies go to the Fluorescent Colony Counting

section of the manual.

Counting Colonies

Quick Capture

Place the Petri dish to be counted on the transillumination surface.

Select the appropriate lighting option for the sample. If unsure, turn the selector switch (located on the front of the
colony counter) to Base Lighting > Trans and remove the black plate (if present). The Trans lighting option will
apply to most applications.

If the colony counter is not already open, double click onto the Doc-It Colony Counter icon on the desktop.

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Insert the Petri dish inside the colony counter.

Click the Preview button in the Camera Control module
and move the Petri dish until it is centered inside the red
circle. The outer red circle should fall just inside the Petri
dish outer edge. If it does not, make sure that the correct
Plate Diameter size was selected.

There are two focusing methods provided for imaging.
The first is Auto focus. Auto focusing allows the camera
to automatically find the appropriate focus for the sample.

Manual focus is provided should the camera need
intervention from the user to more clearly picture the
image.

Manual focus buttons allow users to adjust the focus in

small increments or large increments .

Brightness adjusts the brightness of the image.

Click the Capture button from the Camera Control
module to take a picture.

Click Start Colony Count in the Colony Count module at
the left of the screen to start the counting process.

Select Automated Count or Manual Count. Go to the

Automatic Count section in the manual to complete steps
for automated count. Go to the Manual Count section in

the manual to complete steps for the manual count.

NOTE: The User Defined Template Count is grayed out initially because there are no templates created.
Template counting allows users to create counting templates for frequently counted Petri dish plates. The manual
count process must be performed before template settings can be established.

TIP: The ColonyDoc-It doors can be easily removed if fluorescent colonies will not be counted. Go to the Removing
ColonyDoc-It Doors section in this manual for instructions.

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Lighting Tips:

There are four options for lighting the Petri dish. Epi Lighting options include White light and Blue light and
these sources light the Petri dish from the top. Base Lighting options include Trans and Darkfield and
these sources light the Petri dish from the bottom

Blue light is used to excite GFP stained colonies.

A majority of samples prepared using the spread method and a transparent substrate that are bacterial,
yeast, or mold are best viewed using Base Lighting > Trans.

If there is excessive handwriting on the bottom of the Petri dish, membrane paper, or stickers, then use Epi
Lighting > White or Base Lighting > Darkfield.

Use Base Lighting > Darkfield when counting a pour plate.

Using the black plate on top of the transillumination surface in combination with Epi Lighting sources
provides contrast that improves colony counting results.

Preparing Samples:

When preparing samples, write on the bottom edge away from the center of the Petri dish to increase
counting accuracy.

Before proceeding through the automatic counting steps, ensure that an image of the Petri dish has been captured

and is ready for analysis. See instructions on Quick Capture in this manual for more information on how to capture

an image.

Select Start Colony Count along the
left side of the screen. A new Colony
Count Type Selection window
appears. Select Automated Count
and OK.

Automatic Counting