BIO RAD VERSADOC User Manual



VersaDoc

Imaging System

User’s Manual

for Catalog Numbers

1708010, 1708011, 1708030

1708031, 1708140, 1708141, 1708050, 1708051

Copyright 2001 Bio-Rad Laboratories Inc.

Manual Part Number 4000183 Rev. E

Welcome

Dear Customer,

On behalf of Bio-Rad Laboratories, we would like to thank you for investing in the

VersaDoc
high quality imaging.

One of the best ways to familiarize yourself with the capabilities of your new VersaDoc
system is to read this manual. In it, you will learn how to set up the system and operate
all hardware components. It is also recommended that you read the accompanying
software manual to familiarize yourself with general acquisition functions and data
analysis. After reading this manual, please keep it close to your system so that it can be
conveniently referred to.

Your VersaDoc system is protected by a comprehensive instrument warranty agreement.
Please read this manual thoroughly, so that you fully understand the coverage provided
and are aware of your rights and responsibilities. One of the responsibilities of system
ownership is regular maintenance. Following the maintenance instructions provided with
this manual will help to keep your system and peripherals functioning optimally and will
protect your investment. Please also keep in mind that Bio-Rad offers a range of
comprehensive service agreements that can be tailored to meet your specific needs.

Bio-Rad Laboratories is dedicated to your total satisfaction and would be pleased to
answer any questions that you may have.

How to Contact Bio-Rad Laboratories

In the United States you can reach Bio-Rad Laboratories at the following numbers:

For general information
Toll free: 1-800- 4BIORAD
1-800-424-6723
Fax: [phone]
email: [e-mail]

For service or technical assistance
Toll free: 1-800-424-6723
Fax: [phone]

For information concerning Bio-Rad Laboratories and its products, visit our Worldwide
Web site at http://www.bio-rad.com



Imaging System and we are sure that it will provide you with many years of

Table of Contents

Section 1 General Information PAGE #

1.1 About this Manual 1-1

1.2 Safety Information 1-2

1.2.1 General Cautions 1-2

1.2.2 General Warnings 1-2

1.2.3 Power Safety Information 1-3

1.2.4 UV Safety Information 1-3

Section 2 Introduction

2.1 System Capabilities 2-1

2.2 System Description 2-1

2.3 Mechanical Description 2-3

2.4 Overview of the Imaging Process 2-4

2.5 Illumination Flat Fielding 2-4

Section 3 System Installation

3.1 Operating Requirements 3-1

3.1.1 System Location 3-1

3.1.2 Power Requirements 3-1

3.1.3 Host Computer Recommendations 3-2

3.2 System Setup 3-2

3.2.1 Unpacking 3-3

3.2.2 Shipping Check 3-3

3.2.3 Coupling the Camera Module to the Enclosure 3-5

3.2.4 Installing VersaDoc 1000,3000,4000 3-6

3.2.5 Installing VersaDoc 5000 3-8

3.2.6 Installing the Epi Illumination Modules 3-12

3.2.7 Electrical and Communication Connections 3-13

3.2.8 Installing Filters 3-21

3.2.9 Installing the Lens 3-23

Section 4 System Operation

4.1 Starting the VersaDoc 4-1

4.2 Overview of Operating Steps 4-1

4.3 Detailed Operating Procedures 4-2

4.3.1 Opening the Acquisition Window 4-2

4.3.2 Selecting the Application 4-3

4.3.3 Placing the Sample in the Imaging Chamber 4-3

4.3.4 Lens Selection and Setup 4-4

4.3.5 Aperture Adjustment 4-5

4.3.6 Zoom Adjustment 4-5

4.3.7 Focus Adjustment 4-6

4.3.8 Exposure Time 4-6

4.3.9 Acquiring the Image 4-7

Section 5 Care and Maintenance PAGE #

5.1 General Maintenance 5-1

5.1.1 Cleaning the Sample Platen 5-1

5.1.2 Cleaning the UV Transilluminator Filter Glass 5-1

5.1.3 Cleaning the Lens 5-2

5.1.4 Cleaning the Emission Filters 5-2

5.2 Replacing lamps in Illumination Sources 5-2

5.2.1 Replacing lamps in the Transilluminator Module 5-2

5.2.2 Replacing Lamps in the Epi- illumination Module 5-4

5.3 Lens and Filter Storage 5-5

Section 6 Troubleshooting & Technical Information

6.1 Problem Solving Guide 6-1

6.2 Technical Service 6-3

6.3 VersaDoc System Specifications 6-4

6.4 Warranty Information 6-6

6.5 Glossary of Terms 6-7

6.6 Parts List 6-8

Section 1
General Information

1.1 About this Manual

This manual provides instructions for installing, operating and maintaining the
VersaDoc Imaging System. This manual uses certain conventions to
facilitate understanding of the text material and to assist operators in using the
VersaDoc system.

Conventions

Left and right sides of the instrument are as viewed from the front (operator’s
position) unless otherwise stated.

Commands that are typed in from the keyboard are referred to as <xxxx>, and
when you are expected to use the mouse pointer to activate a button it will be
referred to as CLICK xxxx. When you are expected to click and drag the
mouse to a certain item it will be referred to as SELECT xxxx.

Notes, Cautions and Warnings

Notes, cautions and warnings are used to highlight certain operating
procedures and recommendations.

A note indicates a special procedure, an exception to normal operation or
something else of specific interest to the reader. Notes are preceded by the
word “Note” in italics.

A caution precedes an operational step that could damage the instrument or
destroy data unless the operator takes certain precautions. Cautions are
located in the main text, are preceded by a Caution: statement and are
accompanied by a “Caution Symbol” in the left margin.

A warning precedes an operating procedure that could cause injury to the
operator if not followed correctly. Warnings are located in the main text, are
preceded by a Warning: statement and are accompanied by a “Warning
Symbol” in the left margin.

User’s Manual • 1-1

1.2 Safety Information

This instrument is meant for Laboratory use only and should not be
used in any other way or manner that is not specified in this Manual.

Your safety and the safety of others are very important to us. To help you
make informed decisions about safety, we have provided comprehensive
operating procedures and safety information in this manual and on labels
affixed to instrumentation. This information will alert you to any potential
hazards. It is the user's responsibility to take time and read and understand
the Safety Information and put it to the best use for a Safe operation of the
system.

1.2.1 General Cautions

Caution: Ensure that all of the systems ventilation openings are free of
interference. Excessive heat build up in the instrument may effect performance
or cause operational failure.

Caution: With the exception of cleaning or replacing light bulbs, refer all
servicing to qualified Bio-Rad personnel or their agents. If you experience
technical difficulties with the instrument contact Bio-Rad to schedule a service
appointment. The instrument should not be modified or altered in any way.
Alteration of this instrument voids the manufacturer’s warranty and may create a
potential safety hazard for the user.

Caution: Bio-Rad is not responsible for any injury or damage caused by the use
of this instrument for purposes other than that for which it is intended or by the
modification of this instrument when not performed by qualified Bio-Rad
personnel or an authorized agent.

1.2.2 General Warnings

Warning: This instrument must be connected to an appropriate AC voltage
outlet that is properly grounded.

Warning: There are hazardous voltages inside the rear panel of the

VersaDoc. Do not remove the cover to the Electronics back panel when the

instrument is connected to AC power.

Warning: Do not defeat any instrument interlocks; they are designed to
prevent user injury.

Warning: The
you have purchased. Exercise caution when lifting the instrument. It is
recommended that at least two persons lift the instrument. Lift the instrument
by the bottom plate. Never lift the instrument by opening at the top which is
the plastic camera mounting plate because this will cause light leaks and
damage the camera mounting plate.

VersaDoc weighs 44 kg (96 lbs.) depending on which camera

User’s Manual • 1-2

1.2.3 Power Safety Information

The VersaDoc contains high voltage circuits. The user must disconnect the
power cord prior to opening the rear access panel, or removing the lamp
modules for bulb replacement.

WARNING: It is mandatory for the users to power down the system and
disconnect the AC mains from the unit before performing any disassembly or
repair to the instrument.

The VersaDoc system is designed and certified to meet EN61010 Safety and
EN61326 +A1 Electromagnetic Compliance requirements, which are
internationally accepted safety standards. Certified products are safe to use
when operated in accordance with the instruction manual. This safety
certification does not extend to uncertified equipment or accessories, even
when connected to the VersaDoc system.

Figure 1.1 shows the serial number certification label, which is found on the
rear panel of the VersaDoc system. This label provides manufacturing data
and safety compliance information about the instrument.

Figure 1.1

For easy customer access the instrument serial number information located at
two places in your system.

1. On the rear of the instrument

2. Inside the main door

1.2.4 UV Safety Information

This instrument uses a powerful source of UV radiation and may cause
damage to unprotected eyes and skin. The VersaDoc provides safety
interlocks on both the main door and the sliding UV transilluminator module
to protect the user from accidental UV exposure. A plastic UV shield is
provided for convenience, however, it may not be adequate to protect you
from accidental UV exposure. You must use additional personal UV
protection like UV protective eyeglasses, gowns, gloves etc.

User’s Manual • 1-3

Warning: Do not remove the rear access panel when power is supplied to the
instrument or defeat the UV safety interlock. Attempting to operate the unit
with the cover removed may damage the instrument and expose the operator
to UV radiation.

Warning: Use of controls or adjustments, or performance of procedures other
than those specified herein may result in exposure to hazardous UV radiation.

How to Contact Bio-Rad Laboratories

In the United States you can reach Bio-Rad Laboratories at the
following numbers:

For general information
Toll free: 1-800- 4BIORAD
1-800-424-6723
Fax: [phone]
email: [e-mail]

For service or technical support
Toll free: 1-800-424-6723
Fax: [phone]

For information concerning Bio-Rad Laboratories and its
products, visit our Worldwide Web site at http://www.bio-
rad.com

User’s Manual • 1-4

Section 2
Introduction

2.1 VersaDoc System Capabilities

The VersaDoc Imaging System is a quantitative imaging system for capturing high
resolution digital images from single and multi-color fluorescence,
chemiluminescence, chemifluorescence and colorimetric samples. Using cooled CCD
technology in combination with a unique ultraviolet illumination mechanism and a
highly efficient optical design, the VersaDoc offers researchers the sensitivity,
uniformity, flexibility and dynamic range they require for the analysis of
electrophoretic and microplate samples, among others. With direct imaging and
automated acquisition, this system can increase laboratory throughput and eliminate
the need for chemiluminescent detection using x-ray film.

Flexible Design:

The VersaDoc Imaging system has a very flexible design. The light tight enclosure
can accommodate any of the offered camera modules. The user has the option to
upgrade to any of the four standard models. The standard VersaDoc comes with
every feature included. The VersaDoc 1000L, 3000L, 4000L and 5000L come with
light tight enclosure, camera and filter wheel. The user has the option to choose a
variety of illumination modules to fit their needs. This allows customization of the
system by selecting the type of camera and the type of illumination you need.
Additionally, all systems can be upgraded.

2.2 System Description

Figure. 2.1 The VersaDoc Imaging System.

The VersaDoc combines several key components into a unique, powerful and fully
integrated image analysis system:

User’s Manual • 2-1

(1) Cooled CCD Technology

The VersaDoc system uses cooled CCD technology for image capture and improves
image quality by reducing background noise and enhancing the signal to noise ratio.
This is particularly important for low light chemiluminescence and fluorescence
applications.

(2) Unique Trans and Epi-illumination Source

The VersaDoc system incorporates unique trans and epi-illumination modules for
both UV and white light excitation. This provides high-sensitivity imaging of a variety
of fluorescent, chemifluorescent and colorimetric samples. The broad bandwidth UV
excitation (290-365 nm) supports the detection of a broad range of fluorescent dyes
in contrast to the limited number of dyes, which may be excited using a single
wavelength visible laser.

(3) Interchangeable Lens

The

VersaDoc is supplied with two standard lenses. One zoom and one 50 mm

mono-focal.

Depending upon which VersaDoc system has been purchased, either a 20-40 mm or
the 28-80 mm zoom lens will be included. This zoom lens is ideal for most
fluorescence and colorimetric applications.

The 50 mm, f1.4 fixed lens has a high light collection efficiency and is the lens
recommended for all chemiluminescence applications.

You may purchase an optional 105 mm lens that can be used for imaging small
samples at high resolution. The VersaDoc will accommodate most Nikon f-mount
lenses with a minimum operating distance (MOD) of 0.65 m.

It is highly recommended that lenses be purchased through Bio-Rad, as some Nikon
lenses require modification before they can be inserted into the filter wheel housing.
Use of an unmodified lens may result in damage to either the instrument or lens
mount.

(4) Emission Filters

An eight-position emission filter wheel has been incorporated into the optical design
of the VersaDoc to permit multi-color image discrimination and the detection of many
different fluorescent dyes. The VersaDoc is supplied with four standard filters. Filter
#1 (520LP-Long Pass) is optimized for single color detection of ethidium bromide,
DNAStar, SYBR
Red, SYPRO



Green, SYBR Gold, Radiant Red, SYPRO Orange, SYPRO



Ruby, Texas Red, Cy2, Cy3 and most fluorescein and rhodamine
derivatives. Filters #2 (530BP60) and #3 (610LP) are for the independent detection of
green (fluorescein) and red (Texas Red) fluorescence in multiple colored samples.
These filters effectively support multiplexing analysis for increased sample throughput
and more accurate molecular weight determination. Filter #4 is a clear filter that can
be used for white light applications. Filter positions (Filter #6 #7 & #8) are available to
users for the installation of application specific custom filters. Filter position #5 should
be left vacant for the optimized collection of chemiluminescent samples.

User’s Manual • 2-2

(5) Quantity One 1-D Analysis Software

The Quantity One software permits user-friendly control of the VersaDoc Imaging
System and accurate analysis of the captured image or data. Quantity One is
designed for operation in a Windows or Macintosh environment and supports fully
automated application-based image acquisition.

NOTE: Windows NT does not support USB therefore all WINDOWS NT based systems must use a
Serial Communications port.

The Quantity One package allows substantial flexibility in the presentation of captured
images and provides many tools for data analysis. These include molecular weight
determination, automated lane and band finding, accurate concentration analysis,
VNTR and differential display studies and colony counting. Please refer to the
Quantity One instruction manual for a full description of this software package.

2.3 Mechanical Description

The VersaDoc Imaging System is a modular system and it consists of the following
main hardware components. See figure 2.2.

1. The light tight enclosure, which integrates the sliding UV transillumination module,
two epi-illumination modules, chemiluminescence tray, access to the filter wheel,
lenses and all the electronics needed for controlling the lights and filterwheel.

2. The camera module, which integrates the cooled CCD camera.

3. Depending on which model of VersaDoc you have (1000, 3000, 4000 or 5000),
you will have the corresponding camera module but the light tight enclosure will
be the same.

4. VersaDoc is also available in a "LITE" versions (1000L, 3000L, 4000L or 5000L)
where no illumination sources are included. The unit is offered with a light tight
enclosure and a camera with a filter wheel. All illumination modules, lenses, and
filters are customized for your specific needs.

Light Tight Enclosure Camera Module

Figure. 2.2. Components of the VersaDoc system.

User’s Manual • 2-3

2.4 Overview of the Imaging Process

The acquisition and analysis of image data using VersaDoc technology is a simple
five-part process.

Step 1: Samples to be imaged are placed on the transilluminator module.

Step 2: The appropriate imaging method is selected in the VersaDoc acquisition
window of Quantity One.

Step 3: The sample is aligned using the positioning template in the Quantity One
acquisition window.

Step 4: If required, the imaging lens is zoomed and focused onto the sample to obtain
the highest quality image.

Step 5: The desired collection time for an aperture setting of the lens is selected and
the image is captured. In cases where Flat Fielding is selected, a reference image is
also acquired (see below). Once the sample image is collected and saved, this
Image can then be reviewed and analyzed using the appropriate tools bundled in the
Bio-Rad software package. Please refer to the software manual for further details.

2.5 Illumination Flat Fielding:

A uniform images are essential for quantitative analysis. The VersaDoc Imaging
System features a proprietary algorithm that allows elimination of image non­uniformities caused by lens, illumination source. Optimization of the image uniformity
is made possible via the Illumination Flat Fielding function in the image acquisition
portion of the software.

NOTE: This feature is only for imaging applications that utilize a UV or white
light transillumination source.

Illumination Flat Fielding when using the UV transilluminator:

The software takes an initial image and then prompts the user to remove the sample
and to place the VersaDoc Fluorescent Reference Plate provided with your system
on the UV Transilluminator.

Illumination Flat Fielding when using the white light conversion screen:
The software will prompt the user at the beginning of the image acquisition to place
the VersaDoc white light conversion screen on the UV transilluminator. The sample is
placed on the conversion screen; an initial image is taken. The software then
prompts the user to remove the sample from the VersaDoc white light conversion
screen and then finishes image acquisition.

User’s Manual • 2-4

Section 3

System Installation

3.1 Operating Requirements

3.1.1 System Location

The VersaDoc system should be located in an area that is free of excessive dust or
moisture, strong magnetic fields or ionizing radiation. It is also highly recommended that the
ambient temperature be stable and within the range of 10°C to 28°C (21°C is optimal) and
that the relative humidity not exceed 70%, non-condensing.

Warning: Care should be taken when lifting and moving the VersaDoc system
to avoid personal injury. It is recommended that two people, one on each side
of the instrument lift the VersaDoc enclosure from the bottom.

The VersaDoc should be placed on a level bench top with a minimum depth of 70 cm and a
height clearance of 180 cm, where there is adequate ventilation for the system’s cooling
fans to operate. The system’s feet allow enough clearance for easy removal of your hands
from underneath the instrument once the system has been placed on the bench.

In placing the VersaDoc, users should also allow for easy access to the main power switch,
which is located on the lower right hand side of the system’s rear panel. The instrument
should be placed where there is adequate room to insert the samples into the front of the
enclosure and where it can be easily connected to the host computer. The maximum
distance between the host computer and the instrument should be two meters. (instrument
is supplied with cables long enough for such distances).

Note: The host computer should be located at a workstation that minimizes
operator fatigue.

3.1.2 Power Requirements

The VersaDoc system and its host computer should be connected to a stable grounded
power outlet on a circuit free of electrical noise. In addition, a high quality electrical surge
suppressor/line filter with a 10 Amp or higher rating should be used to avoid damage from
AC fluctuations. Only a grounded 3-pin power cord should be used to connect power.

The VersaDoc is designed for operation at an input voltage of 110-240 VAC, at 50-60 Hz.

Deviation from these operating voltages can lead to slower cooling and heating
process with your deeply cooled CCD camera.

User's Manual • 3-1

3.1.3 Host Computer Recommendations

The VersaDoc system is capable of producing large image files of high resolution to easily
handle such large files. A powerful computer is required.

Please refer to your software manual for detailed host computer system and software
requirements. If the computer is not purchased from Bio-Rad, systems compatibility is the
responsibility of the user. Please check with your local Bio-Rad office regarding
compatibility for your specific brand of computer.

3.2 System Setup

There are 3 main phases in the installation of the VersaDoc system:

1. The components are delivered to your laboratory.

2. The system is installed by a trained Bio-Rad representative.

3. Users are trained on the operation of the VersaDoc and accompanying peripherals and
software by a Bio-Rad representative.

The following steps for setup of the VersaDoc requires approximately two hours.

Prepare the VersaDoc hardware:

1. Unpack components

2. Perform shipping check

3. Install the camera module

4. Install the transilluminator module and epi-illumination modules

5. Connect system cables

6. Install emission filters

7. Install lens

8. Connect electrical and host computer communication cables

9. Power up the instrument

Each of these steps is detailed in the following sections.

User's Manual • 3-2

3.2.1 Unpacking the VersaDoc System Components

With the exception of operating software, VersaDoc components are shipped in pallet­supported boxes. Unpack the components by following the steps listed below:

1. Cut the two steel straps supporting the main instrument package.

2. Remove the top cardboard lid. Remove other packaging materials and secondary boxes

from the top.

3. Slide the outer sleeve off the box vertically. The VersaDoc enclosure can be found
within the box.

4. With the assistance of a helper, remove the VersaDoc from the box. Grip the bottom of
the enclosure on both sides (do not lift the instrument by the front door or electronics
area) and place it on the floor for the next step in the setup procedure. When placing
the enclosure allow clear access to the rear panel for connection of the appropriate
cables.

Warning: Get a helper; a single person should not attempt to lift the VersaDoc.

Warning: To avoid back injury, always bend your knees and keep a straight

back when lifting heavy objects.

Caution: Do not supply power to the instrument until the VersaDoc system has
been set up using the following installation procedures.

5. Open all the other boxes and carefully remove all the items.

6. Perform a shipping check to confirm that the system has been supplied complete.

3.2.2 Shipping Check

During the unpacking process inspect all shipping containers to ensure that you have
received all ordered items and that no boxes are damaged. If items are either missing
or damaged, this should be noted at the time of installation so that it can be immediately
reported to both the shipping company and Bio-Rad manufacturing.

The Quantity One acquisition and analysis software is supplied in a separate box.

User's Manual • 3-3

The VersaDoc hardware should arrive complete with the following items:

Quantity Item Photo

1 VersaDoc light tight enclosure

1 VersaDoc camera module (Shown Model

1000 camera module, model 3000, 4000
and 5000 are shown later in this section)

1 VersaDoc transilluminator module (already

installed inside the light tight enclosure)

1 Pair of UV epiilluminator modules

1 Pair of White epi illuminator Modules

1 Sample/chemi tray

1 Camera power cable (VersaDoc 1000 and

4000 only)

Or

Fan assembly power cable (VersaDoc 5000
only)

1 Camera AIA interface cable

1 Serial/USB communication cable

User's Manual • 3-4

Quantity Item

1 Sample Holder Kit
1 VersaDoc Fluorescent Reference Plate
1 PCI Digitizing Card
1 White Light Conversion Screen (Optional)
5 Filters (530DF70, 520LP, 610LP, Clear, 660Cutoff)
2 Lenses (20-40mm Zoom, 50mm Fixed)*
2 Lenses (28-80mm Zoom, 50mm Fixed)* *
1 Lens and Filter Cleaning Kit
1 Focusing Target
1 Power Cord
1 Instruction Manual
1 Camera Specification File (CD)
1 58mm-52mm Step Down Ring**
1 Warranty Card

* These are provided with VersaDoc 1000 model only
** These are provided with VersaDoc 3000, 4000 and 5000 models

NOTE: Please retain all packaging materials for future transport of the
VersaDoc system. Additional charges will be assessed if packaging is not
available for instrument warranty shipping.

3.2.3 Coupling the Camera Module to the enclosure:

This applies to all camera modules (VersaDoc 1000, 3000, 4000 and 5000). Follow

the procedure outlined below to mount the camera module to the enclosure.

1. Leave the enclosure on the floor for easy access to the camera mount.

2. Correctly position the camera module on the camera mount located at the top of
the enclosure such that the three holes in the camera module adapter plate will
match the three standoffs located in the filter wheel assembly in the camera
mounting plate.

NOTE: The camera module should sit completely flat and square on the
surface of the Enclosure to avoid light leaks

3. Using the 3 cap-head screws and the 9/64” hex key (included), secure the
camera adapter plate to the standoffs. Carefully tighten the screws evenly to
form proper light seal. See figure 3.1 for details.

.

User's Manual • 3-5