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VersaDoc User Manual
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1. Location uit a tems will be installed in the folder Applications Mac 0S 937 an the disk untitled Install Location untitled Depending upon the Imaging device you are installing click on the desired Imager you want to install and then click on Install The drivers will get loaded and at the completion of the installation the following window will open Installation was successful You have installed software which suggests you restart your computer if you are finished click Restart or click Quit to leave the Installer Ifyou wish to perform additional installations click Continue User s Manual e 3 18 k Click on RESTART so that the system will start and will now restart Please read the README file before using the system elcome to Quantity One 4 5 hank you for installing Quantity One 1 D analysis software hardware security key HSI is included with this ersion of Quantity One Before continuing with installation be sure the HSK is plugged in to an available USB port Note that the download version of Quantity One has a fee 30 day trial period during which you do not nonnally need an HSK After the trial period expires you can continue o use Quantity One in Basic mode See the Release Notes and User Guide for more information his installer also installs Solobug TDS Please use Solobug for reporting any feature requests or design changes See t
2. 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
3. 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 VersaDoc weighs 44 kg 96 Ibs depending on which camera 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 User s Manual e 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 VersaDo
4. high NA lens follow the procedure outlined below Figure 3 21 1 Remove the lens from its packaging and retain the packaging for future storage Remove the protective cover from the lens mount rear of lens and check that the lens is clean free of dust fingerprints and scratches If the lens is dirty it should be cleaned with the materials provided in the lens and filter cleaning kit Open the door to the main door and position the lens so that the white line and dot on its mount matches the white mark on the base of the camera assembly Insert the mount of the lens into the base of the camera assembly and turn the lens clockwise to the left until you hear it click The main white line and lens settings are directly in front of you User s Manual e 3 24 Figure 3 21 Steps in 50 mm lens installation 5 The lens in now locked into position and the lens cap and protective platen cover can be removed Lens Removal To remove the lens from the camera housing follow the procedure outlined below Figure 3 22 1 Place the lens cap on lens 2 Hold the lens firmly with your left hand throughout the remainder or the removal process so that it cannot be dropped accidentally Caution Accidentally dropping the lens could break the UV transilluminator platen or white light conversion screen Replacement of such a broken platen or white light conversion screen is not covered by warranty or service contract 3 Depress t
5. lamps by holding the metal part of the lamps with the tip of your fingers and turning them in a rotating movement and by pulling them out of the socket See Fig 5 2 AE ETA Remove hex standoffs X4 Remove the baffle exposing the lamp Hold at the metal ends of the lamps and turn to remove Figure 5 2 9 Install the replacement lamp by inserting its ends in the sockets and rotating until it clicks into place 10 Now reinstall the baffles on the lamps by making sure that they are seated correctly 11 Reinstall the cover on the transilluminator module Replace the screws 12 Carefully reinstall the transilluminator assembly back onto the slides by carefully lining up the slides into the guides and then gently push in all the way NOTE There is no need to push down or up on the levers they are only used to remove the transilluminator assembly User s Manual e 5 3 13 Next carefully connect the UV transilluminator cable back to the ballast assembly Turn the power ON to the system 14 Make sure that the door is closed 15 Try an application that requires use of UV transilluminator to make sure that the new lamps are fully operational 5 2 2 Replacing lamps in the Epi illumination module Tools required You will need a size 3 32 hex allenkey to change the lamps in the epi illumination module The VersaDoc has two epi illumination modules each contain single white illumination source and broad ban
6. 00 4000 and 5000 models NOTE Please retain all packaging materials for future transport of the This applies to all camera modules VersaDoc 1000 3000 4000 and 5000 Follow 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 the procedure outlined below to mount the camera module to the enclosure 1 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 Leave the enclosure on the floor for easy access to the camera mount 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 e 3 5 Three cap head screws to secure the camera to the filter wheel assembly Figure 3 1 Installing VersaDoc 1000 3000 4000 Connecting the Cables to the Camera Module This procedure applies to the Versa Doc 1000 and 3000 and 4000 systems Connecting the camera power cable Camera power cord has a DIN connector on each end The cable with a 9 p
7. Doc from electrical power prior to cleaning the external surface of the instrument 5 1 1 Cleaning the Sample Stage Area The sample platen and sample stage of the VersaDoc should be cleaned between imaging sessions to optimize image quality Use powder free gloves when cleaning the instrument to avoid fingerprints that may appear during imaging Never wear powdered gloves when cleaning the VersaDoc Clean the sample platen with optical cleaning solution and a lint free optical tissue Cleaning kits are available from Bio Rad and one is supplied with the instrument Caution It is recommended that water mild liquid soap and a soft sponge are used to clean the sample stage Never use abrasive cleaners solvent based detergents or scouring pads to clean the platen surface 5 1 2 Cleaning the Transilluminator Platen The platen on the transilluminator module should also be periodically cleaned to remove dust and optimize image quality To clean the platen follow the steps outlined below 1 Turn off the VersaDoc 2 Open the main door and slide out the transilluminator assembly 3 Clean the top platen using optical cleaning solution and optical tissue 4 Once the platen is clean push the transilluminator back into the enclosure User s Manual e 5 1 5 1 3 Cleaning the Lens To optimize image quality it is recommended that any lens used with the VersaDoc be cleaned before it is installed in the system Both sides of the lens should be clean
8. Manual e 3 20 Power On Sequence Normally the VersaDoc system should be switched on for 30 seconds before The host computer is powered up This protocol is required for the computer to recognize the VersaDoc as a peripheral device 1 Power up the VersaDoc system first 2 Also power up the power supply block in case of the VersaDoc 3000 or CEU in case of the VersaDoc 5000 system 3 Power up the PC Mac second 4 In case of a PC the VersaDoc system is detected via USB connection A new window will indicate that a new USB device has been found 5 Proceed to the next step to complete the installation 3 2 8 Installing Filters The VersaDoc is supplied with three emission filters and one clear filter These must be installed in the 8 position filter wheel before use These filters are 1 520LP Long Pass Used for most single color fluorescent stains and labels 2 530BP Band Pass Used for detection of green signal FITC etc in multi color fluorescence experiments 3 610LP Long Pass Used for detection of red signals Texas Red etc in multi color fluorescence experiments 4 Clear Used for system focus and some colorimetric applications To install the filters follow the procedure below Figure 3 19 1 Ensure that all power and communication cables are connected and that the VersaDoc system is turned on NOTE Do not power up the PC or MAC yet 2 Open the main door This will expose the camer
9. One Setup 15 x Welcome to the Quantity One Installation Wizard It is strongly recommended that you exit all Windows programs before running this setup program ad Click Cancel to quit the setup program then close any programs Di S c oOV ery you have running Click Next to continue the installation L WARNING This program is protected by copyright law and Seri es international treaties Unauthorized reproduction or distribution of this program or any portion of it may result in severe civil and criminal penalties and will be prosecuted to the maximum extent possible under law Cancel b Click on NEXT the following window will open ig Quantity One Setup 5 xj Select Features BIO RAD Please select which features and instrument drivers you want to install Feature Description Support drivers for the Hardware Security Key HSK X vj CFR Service This feature will be installed on the local hard drive This feature requires 1744KB on your hard drive Browse Wise Installation Wizard 5 Disk Cost Reset lt Back Cancel User s Manual e 3 15 c Click on the arrow next to ChemiDoc XRS VersaDoc drivers to get installer options See picture below ox Select Features BIO RAD Please select which features and instrument drivers you want to install Quantity One HSK Support X Gel Doc EG ChemiDoc E
10. Q Drive EFi ChemiDoc XASVersaDoc Driver willbe installed on local hard drive 8 Entire feature will be installed on local hard drive Feature Description Support drivers for the ChemiDoc AS VersaDoc Imaging Devices ain uninstalled Entire Feature will be unavailable OKB on your hard drive x d If you are installing the drivers on local drive select appropriate option by scrolling down as shown in the picture below Click on NEXT E Quantity One Setup rt Select Features B O Please select which features and instrument drivers you want to install BIO RAD Quantity One HSK Support Gel Doc EQ ChemiDoc EQ Drive ChemiDoc XRS ersaDoc Driver Feature Description Support drivers for the ChemiDoc AS VersaD oc Imaging Devices talled on the local hard Entire Feature will be unavailable 298KB on your hard drive x Browse Wise Installation Wizard Disk Cost Reset Cancel User s Manual e 3 16 e Drivers will be copied to the appropriate location on your hard drive and at the completion the following window will appear ig Quantity One Setup Quantity One has been successfully installed Click the Finish button to exit this installation Discovery Series f Click on FINISH and the system will shut down At this time install the PCI card into the system and REBOOT the system g As the syste
11. VersaDoc Imaging System em 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 TM VersaDoc Imaging System and we are sure that it will provide you with many years of 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 tailo
12. a 2 Phillips screwdriver and 5 16 size socket wrench to change the lamps in the transilluminator To change the lamp follow the procedure outlined below Figure 5 1 1 Turn off the power to the system 2 Open the main door to access the UV transilluminator cable 3 Disconnect the UV transilluminator cable from the ballast assembly 4 Slide the UV transilluminator module on the slides out completely 5 There are two release levers on each rail that are made out of black plastic Pull the transilluminator module out while pressing down on the lever on the right side and lifting up the lever on the left This will allow you to completely disengage the slide rails from User s Manual e 5 2 the guides rails located in the enclosure and the entire transilluminator module will become free from the enclosure re BE F Release lever for slides Transilluminator Transilluminator without the cover Figure 5 1 6 Using the Phillips screwdriver remove the cover assembly from the transilluminator by removing four screws There are two screws on each side of the cover 7 Using the 5 16 socket wrench remove the four hex standoffs that hold the baffles on the lamps of the transilluminator and then gently lift off the baffles exposing the transilluminator lamps Note Be careful and do not bend the baffles because bending the baffles could lead to deterioration of uniformity of your UV transilluminator 8 Remove
13. a filter assembly filter advance button and the lens mount assembly 3 Loosen the left side screw of the filter wheel cover and remove the right side thumbscrew completely by fully unscrewing it The cover can now be rotated downward to expose the filter wheel 4 Push the filter advance button until filter position 1 is in the center front position The 1 label should be clearly visible on both sides of the filter slot User s Manual e 3 21 5 Remove filter 1 from its packaging and check that it is clean free of dust fingerprints and scratches If the filter is dirty it should be cleaned with the materials provided in the lens and filter cleaning kit 6 Holding the filter by the numbered tab with the number in the correct orientation carefully slide the filter into the open filter wheel position 7 Repeat steps 4 5 for the remaining filters 2 3 4 8 Replace the filter wheel cover and hand tighten both captive thumbscrews 9 Close the main door firmly The filter wheel will automatically reset to the home position and is now ready for operation NOTE The above procedure can also be used for the installation of custom filters Open filter wheel access panel and rotate it downward as shown Unpack and carefully install filter 1 Make sure that filter 1 is all the way in its slot and positioned straight Figure 3 19 User s Manual e 3 22 3 2 9 Installing the Lens The VersaDoc system is supplied wit
14. al 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 sy
15. ange 3 4 orders Illumination Flat Fielding Yes User s Manual e 6 4 VersaDoc 4000 Cooled CCD Specification Imaging array 2184 X 1472 Pixel size 6 8 x 6 8 micron Pixel depth 12bit Detector type Scientific grade high sensitivity front illuminated CCD with antireflective coating and micro lenses Cooling system Forced air peltier thermoelectric system Cooling range 10 C 2 C Dynamic Range 3 4 orders Illumination Flat Fielding Yes VersaDoc 5000 Cooled CCD Specification 7 Imaging array 512 x 512 Pixel size 24 x 24 micron Pixel depth 16bit Detector type Scientific grade high sensitivity back illuminated CCD with antireflective coating Cooling system Forced air peltier thermoelectric system Cooling range 25 to 35 C 2 C Dynamic Range 4 8 orders Illumination Flat Fielding Yes User s Manual e 6 5 6 4 VersaDoc Warranty Information This warranty statement may vary outside of the continental United States Please contact you local Bio Rad office for the exact terms of your warranty Bio Rad laboratories warrants to the customer that the VersaDoc system catalog number 1708013 or 1708033 1708143 or 1708053 will be free from defects in material and workmanship and will meet all of the performance specifications for a period of one year from the date of shipment This warranty covers all parts and labor If any defects should occur during this period Bio Rad Laboratories will either rep
16. ard in the system before loading the drivers click on CANCEL when WINDOWS prompts you to point at the drivers for new HARDWARE it has found Follow the steps for installing the software and loading the drivers as shown above and reboot the system to properly install the card and drivers to your MAC or PC as the case maybe Should you forget to click on CANCEL when windows prompts you that it has found new HARDWARE It will search for the drivers and then render the card as DISABLED To recover from this take the following steps 1 2 3 4 Install the drivers as shown in the procedure above Go to ADD REMOVE HARDWARE utility in the CONTROL PANELS Click and highlight the PCI card in question Roper or Scion and click on REMOVE Follow the prompts and reboot the system Windows will now find the card and install the drivers as described above 6 2 Technical Service For technical assistance with the VersaDoc system including all hardware and software contact your local Bio Rad office or in the US call 1 800 424 6723 All spare parts not listed in this document can be ordered by contacting your local Bio Rad office For inquiries and requests regarding system repair or service contact your local Bio Rad office or distributor in the U S call Technical Service at 1 800 424 6723 Please have the following details available 1 Instrument model and catalog number 2 Serial number located on the back of th
17. ation 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 e 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 clearan
18. c 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 m input Vettege Frequency Model Serial No Weximum Rated Power fioo 240 vac 0 60 Hz Versaboc Imoging System 1000 sa00R sew A A Ale c Mode in USA P N 4200860 Rev A Node For service or technical assistance contact Bio Red Loboretories Serial No Toll free 1 800 424 6723 jah Semmes 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 n
19. ce 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 e 3 1 3 1 3 Host Computer R
20. 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 Slide the outer sleeve off the box vertically The VersaDoc enclosure can be found within the box 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 com
21. connector located at the top surface of the electronics module See picture 3 13A For units with serial number xxxBR300 or higher Connect the fan power cable from the fan assembly 5000 models only to the DB9 power connector located on the side of the electronics module Once connected the system cable User s Manual e 3 11 connections will look similar to the ones shown in Figure 3 13 A or B depending on th eserial number of the enclosure you may have EI 13 Fig 3 13 B _ _ Fan Cable ICK Figure 3 13 3 2 6 Installing the Epi modules 1 Remove the access panel mounted on the ballast panel by unthreading the two thumbscrews Thumb screws on the ballast panel Figure 3 14a 2 If not connected already connect the transilluminator cable to the connector labeled UV TRANSILLUMINATOR located on the ballast panel on interior rear wall of the enclosure 3 To install the epi UV and white modules first install the epi UV module by inserting the two prongs on its end plate to the slots located at the back wall 4 Secure the module using the captive screw by lining up the front side of the module with the hole located in the wall of the instrument See Figure 3 14b 5 Now connect the cable from the epi UV module to the appropriate connector on the ballast assembly User s Manual e 3 12 Tongue and Groove mechanism to hang EPI WHITE from EPI UV Threaded insert f
22. directly into the imaging chamber on the UV transilluminator platen With wet samples you will find it convenient to use the sample holders provided with your VersaDoc system These sample holders have suction cups that hold the sample in place and keep it from sliding around on the polished glass surface Caution The sample stage area is resistant to most research chemicals but may be damaged by extended contact with strong acid solutions and organic solvents When imaging samples exposed to these chemicals users should wash the sample stage with water and wipe dry immediately after imaging Samples should be placed in the VersaDoc instrument following the steps outlined below Open the main door Visually check that the sample platen is clean If not clean using an optical cleaning solution and a soft lint free towel or lens cleaning tissue From the VersaDoc acquisition window select the POSITION function in Step Il Figure 4 1 The image display window will now present a real time image of the sample in the chamber that refreshes rapidly Position your sample on the imaging platen using the software generated alignment grid to ensure that it is correctly placed and in the center of the viewing area Note When imaging fluorescent gel samples it is recommended that the sample be removed from the glass or plastic plates of the gel sandwich for good image quality The glass and plastic will fluoresce when exposed to UV light and will cont
23. dwidth UV sources It is recommended that lamps in both the right and left epi assemblies must be replaced at the same time To change an epi lamp follow the procedure outlined below Figure 5 3 NOTE The procedure to remove and replace the lamp in the UV or white light epi modules is the same The procedure outlined below applies to both 1 Turn off the VersaDoc and disconnect all power removing the power cable 2 Open the door to the sample compartment 3 Find the threaded mounting screw that secures the epi modules to the wall of the enclosure and loosen it to free up the epi module from the wall 4 Disconnect the epi module cables from the ballast assembly and remove the epi module completely from the unit and set it on a clean bench 5 Using a hex 3 32 key remove the three screws that secure the front end plate on the epi modules and slide out the end piece and filter glass and set aside for future use See Figure 5 3 Remove the end plate using View of the epi end Filter glass end plate allen key 3 cap head 3 32 Allenkey plate screws and the end piece Figure 5 3 User s Manual e 5 4 6 This exposes the lamps in the epi module for you to replace To replace the white light lamp or UV lamp simply grab the two metal ends of the old lamp and carefully rotate to release it from the sockets See Figure 5 4 Remove lamp by grabbing the two metal ends and turning t
24. e bottom right of the rear panel Figure 3 16 VersaDoc Connections The VersaDoc is connected to the host computer via a Serial or USB interface and an AIA interface One each of the Serial and USB port is located on the rear right side of the unit Use the supplied USB or Serial Cable to connect the PC to the VersaDoc Caution To prevent damage to the hardware all instruments must be turned off before attempting to connect or disconnect the unit to the host computer Upon insertion of the Serial or USB cable into the VersaDoc the Serial or USB port the PC will automatically select operation and sense the presence of VersaDoc NOTE Do not turn ON the power to the VersaDoc and CEU in case of VersaDoc 5000 yet User s Manual e 3 14 Connecting the AIA Cable to the Computer To do this two things must happen i The software must be installation on the PC which will control this system ii The PCI Digitizing card must be installed into the PC where the AIA cable is to be connected Software Installation Please follow the instructions below to install the PC or Mac software for VersaDoc system NOTE Do not install the PCI card into the PC yet First install the drivers as shown below and then install the PCI Card PC based VersaDoc systems a Insert The Discovery Series software CD into the CD ROM drive of the PC It will go into AUTO RUN mode and the following window will open ig Quantity
25. e 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 e 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
26. e main door 3 Hardware firmware and software version information in operating software About box User s Manual e 6 3 6 3 VersaDoc System Specifications System Technical Specifications Specification Light source Transillumination UV 290 365 NM and white light 400 750 NM Epi illumination UV 290 365 NM and white light 400 750 NM Emission filters 8 position filter wheel 520LP 530DF70 610LP and clear filters supplied Transillumination area 25 x 25 cm Operating Conditions Supply voltage 100 120 or 220 240 VAC 10 Frequency 50 60 Hz Operating Temperature 10 28 C 21 C recommended Operating Humidity Relative lt 70 non condensing Dimensions 23 W x 26 D x 39 H Total Weight 96 Ibs VersaDoc 1000 Cooled CCD Specification Imaging array 1317 X 1035 Pixel size 6 8 x 6 8 micron Pixel depth 12bit Detector type Scientific grade high sensitivity front illuminated CCD with antireflective coating Cooling system Forced air peltier thermoelectric system Cooling range 10 C 2 C Dynamic Range 3 4 orders Illumination Flat Fielding Yes VersaDoc 3000 Cooled CCD Specification i Imaging array 1536 X 1024 Pixel size 9 x 9 micron Pixel depth 12bit Detector type Scientific grade high sensitivity front illuminated CCD with antireflective coating Cooling system Forced air peltier thermoelectric system Cooling range 25 C 2 C Dynamic R
27. ecommendations 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 Unpack components Perform shipping check Install the camera module Install the transilluminator module and epi illumination modules Connect system cables Install emission filters Install lens Connect electrical and host computer communication cables Power up the instrument OCAONOARWN gt Each of these steps is detailed in the following sections User s Manual e 3 2 3 2 1 Unpacking the VersaDoc System Components With the exception of operating software VersaDoc components are shipped in pallet supported boxes Unpack the
28. ed The 50 mm high NA f 1 4 lens is designed for optimized light collection efficiency and will produce superior images for all low intensity chemiluminescence experiments The lens can also be used for collecting typical fluorescence and colorimetric images however the imaging area is fixed This lens is designed to work in combination with the chemiluminescence sample tray placing the sample closer to the camera for improved light collection efficiency Infrared Cutoff Filter When performing any fluorescence experiments it is recommended that the 660 nm infrared cut off filter that is supplied with the VersaDoc be installed on the front of collecting lens see figure 4 3 This filter will block any infrared signal that may be generated by the UV bulbs substantially reducing image background and improving sensitivity This filter is not required for chemiluminescence experiments and should not be present when collecting low intensity chemiluminescence signals as it will reduce the amount of signal collected Figure 4 3 User s Manual e 4 4 Aperture Ring Zoom Ring Focus Ring Zoom Lens 50 mm Fixed focal length lens FIGURE 4 4 4 3 5 Aperture Adjustment The aperture or f stop ring is located at the top of the lens Figure 4 4 and controls the amount of light that passes through the lens to be captured by the CCD camera When the aperture is fully open the f stop number will be smallest the depth o
29. ed using an optical cleaning solution and optical tissue Avoid touching the glass surfaces of the lens when installing it into the instrument as fingerprints will effect image quality 5 1 4 Cleaning the Emission Filters To optimize image quality it is recommended that the emission filters installed in the VersaDoc system are periodically cleaned Both sides of each emission filter should be cleaned using an optical cleaning solution and optical tissue Avoid touching the glass surfaces of the filter when installing it into the instrument as fingerprint will effect image quality 5 2 Replacing Lamps in Illumination Sources The life of the broad wavelength UV lamp is approximately 500 to 1000 hours depending upon use As the lamp ages the required integration time will increase because the intensity of the UV emission will diminish If the integration time for image acquisition has increased more than three fold it is recommended that the lamps be replaced The life of the white light lamp is approximately 1000 hours NOTE THE LAMPS SHOULD BE REPLACED IN PAIRS FROM ALL ILLUMINATION MODULES 5 2 1 Replacing the Lamps in the Transilluminator Module To access the lamps in the transilluminator follow the procedure outlined below Caution Do not touch the glass parts of the lamp or lamp housing Fingerprints on the lamp may result in non uniform illumination The use of power free latex gloves is highly recommended Tools required You will need
30. el of the VersaDoc will flash during acquisition to indicate that the image is being captured The software will automatically set all instrument collection parameters and prompt you to take additional steps for best results NOTE You will notice that after the initial image capture the software also acquires a dark image This image is taken for the same amount of time as the exposure however this dark image is acquired with the camera shutter closed This provides a very accurate way to measure and remove the dark current noise from the image Once the image is captured it will be displayed in its own window You may save the captured image for storage and or future analysis NOTE When an application is selected that utilizes UV transilluminator the software will first acquire an initial image and then prompt you to remove the sample You must make sure that the sample platen is free of any solution from the sample You will then be prompted to place the VersaDoc Fluorescent Reference plate When your application requires white light transillumination the software will also prompt you to place the VersaDoc white light conversion screen on the UV transilluminator platen This white light conversion screen absorbs the UV from the UV transilluminator and converts this broadband UV into white light See figure 4 5 Figure 4 5 White Light Conversion Screen In this application the software will first take an initial image and then prom
31. ence and all warranties of merchantability fitness for a particular purpose otherwise expressed or implied in fact or by law and state Bio Rad s entire and exclusive liability and the buyers exclusive remedy for any claims or damages in connection with the furnishing of goods or parts their design suitability for use installation and operation Bio Rad Laboratories will in no event be held liable for any special incidental or consequential damages whatsoever and Bio Rad s liability under no circumstances will exceed the contract price for the goods for which liability is claimed User s Manual e 6 6 6 5 Glossary of Imaging Terms CCD Charge Coupled Device CCD Element Each CCD element or pixel is a single photodetector capable of detecting light and converting and storing the information in an electronic form CCD Array A CCD array can be visualized as a periodic grid array of individual CCD elements analogous to buckets of water When the shutter is open photons of light analogous to drops of rain fall into the photo detectors buckets of water Integration When the camera shutter is open and the CCD is exposed to light Thermoelectric A thermoelectric cooler TEC that pulls heat away from the CCD Cooler The heat is then transferred to the camera body which is cooled by forced air Dark Current Dark current arises from the creation of electrons generated through the process of thermal emission within the silic
32. era 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 amp 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 Term
33. etting can be adjusted and viewed in real time by selecting the POSITION function in the VersaDoc acquisition window The image display window will now show a real time image of the sample as it will be captured This image refreshes every second to help you optimize your zoom settings Note The 50 mm lens offers no zoom adjustment User s Manual 4 5 4 3 7 Focus Adjustment To focus the lens on the sample for sharp images you must choose the FOCUS button in the Quantity One acquisition window This button allows focusing on a small part of the image When using this mode the white epi lights turn on automatically and the shutter is opened and closed repeatedly and the acquisition window is continuously updated to allow you to focus your lens on the sample The exposure time during the focus mode is adjusted automatically to allow proper unsaturated images If during focus mode the images still show up saturated then you must adjust the aperture to a lower setting to view the images in the focus mode If the images still show up as saturated all white then you may turn off the epi lights by clicking on the button labeled Lights On see figure 4 1 This will turn off the white lights and now you may open the main door and adjust the focusing ring See Figure 4 5 on the lens to achieve a sharp focus on your sample 4 3 8 Exposure Time The exposure time refers to the period of time that the shutter will remain open and light will pass fr
34. f field will be the lowest and the most light will pass through the lens When the aperture is fully closed the f stop number will be largest the depth of field will be highest and the least light will pass through the lens For low signal applications such as chemiluminescence it is recommended that the aperture be fully opened to the smallest f stop value Note When the aperture on the zoom lens is fully closed largest f stop setting of 22 the aperture ring locks To unlock the aperture ring push the black release button to the right of the f stop indicator while turning the ring to the right counter clockwise Note The aperture ring on the 50 mm lens will not lock in the fully closed f stop 16 position unless the user activates the lock mechanism on the lower right hand side of the f stop indicators To lock in this position move the button white dot up so that it aligns with the orange indicator It is not recommended that the lens be locked in this position for chemiluminescence experiments as this setting allows the least light through the lens 4 3 6 Zoom Adjustment When using the zoom lens the view area of the image can be adjusted by rotating the zoom ring Figure 4 4 The zoom ring is located directly below the aperture ring At maximum zoom the indicator on the lens will be set to its highest specified focal length 40 or 80 mm depending on which lens is being used also the image resolution will be at its best The zoom s
35. h two standard lenses a flexible zoom lens and a high NA 50 mm lens with improved collection efficiency Zoom Lens for fluorescence and colorimetric imaging The Tamron zoom lens is recommended for use with all fluorescence and colorimetric applications and for high intensity chemiluminescence experiments The zoom capabilities of this lens supports the imaging of small and large samples The zoom lens is not a high numerical aperture NA lens and should not be used for low intensity chemiluminescence experiments High Numerical Aperture Lens for Chemiluminescence Imaging The Nikon 50 mm high NA f 1 4 lens is designed for optimized light collection efficiency and should be used for all low intensity chemiluminescence experiments The lens can also be used for collecting typical fluorescence and colorimetric images The chemiluminescence sample tray may be used to move the sample closer to the camera Infrared Cutoff Filter When performing any fluorescence experiments it is required that the 660 nm infrared cut off filter that is supplied with the VersaDoc is installed on the front of collecting lens This filter will block any infrared signal that will be generated by the UV bulbs substantially reducing image background and improving sensitivity This filter is not required for chemiluminescence experiments and should not be used when collecting low intensity chemiluminescence signals as it will reduce the amount of signal collected Len
36. he Release Notes or on line Help for more information oe Ceoncmue Installing the PCI digitizing card to the PC Caution Ensure that the VersaDoc system is turned off before Installing the digitizing card and AIA cable 1 Now install the digitizing card into a PCI slot in your computer and secure it with appropriate screw See Figure 3 17 PCI digitizing card PCI slot inside the PC Figure 3 17 2 Connect the camera to the digitizing card with the AIA cable Do not power up the PC MAC yet See section 3 2 9 for powering up the PC User s Manual e 3 19 3 With both Serial or USB and AIA cables connected your system will appear as shown in one of the figures 3 18 a e below yp Power Cable I AIA Cable Fan Cable Control Cable Serial USB T a AIA Cable Figure 3 18a VersaDoc 1000 3000 and 4000 Systems under Serial xxxBR300 Figure 3 18b VersaDoc 5000 System under Serial xxxBR300 r AIA Cable Power Cable 1 Serial USB Power Supply Fan Cable Control Cable n Serial USB s miin TES AIA Cable F Figure 3 18c VersaDoc 3000 Systems starting Serial xxxBR300 Figure 3 18d VersaDoc 5000 System starting Serial xxxBR300 Camera Power Cable l En Serial USB e f AIA Cable i Figure 3 18e VersaDoc 1000 and 4000 Systems starting Serial xxxBR300 User s
37. he lamp to release from its socket Figure 5 4 16 Install the replacement white light lamp by placing its ends in the sockets and rotating until it clicks into place Be careful not to touch any glass surfaces of the lamp or the filter glass Use of latex gloves is highly recommended 17 Carefully rotate the lamp to make sure it is seated properly 18 Now reinstall the filter glass end piece and the end plate Secure the end plate properly using the 3 cap head screws and the 3 32 hex Allenkey 19 Reinstall the epi module in its place and reconnect epi cables to the ballast assembly to appropriate connectors 20 Now power up the system and try running the application that use the epi source in which the lamps were installed to make sure that the lamps are operating normally NOTE THE UV INTERLOCK ON THE MAIN DOOR WILL NOT ALLOW UV EPI TO TURN ON ACQUIRE AN IMAGE OF A WHITE PIECE OF PAPER TO ENSURE THAT THE EPI UV LAMPS THAT YOU JUST INSTALLED ARE WORKING PROPERLY IF NO IMAGE COMES UP YOU MAY HAVE A POORLY SEATED LAMP IN THE SOCKET To order replacement lamps contact your Bio Rad Laboratories representative for parts 5 3 Lens and Filter Storage Always store unused lenses and filters in their original box and in a low humidity environment with a stable ambient temperature that does not exceed 30 C Lenses should be wrapped in optical tissue before being placed in their storage box If your laboratory is a high humidity e
38. he red release button on the base of the camera housing This is located to the rear right hand side of the lens 4 Rotate the lens in a clockwise direction to the right to release it from the housing 5 Pull the lens down and remove it from the filter wheel assembly 6 Replace the mount cover If the lens is not being used for some time it is recommended that it be stored in its original packaging User s Manual e 3 25 nite 7 W a CELA TE Figure 3 22 Steps in lens removal Proceed to section 4 User s Manual e 3 26 Section 4 Operating the VersaDoc 4 1 Starting the VersaDoc System Both the VersaDoc and the camera module must be connected to the computer prior to using the VersaDoc system To turn on the VersaDoc press the power switch located on the right hand side of the rear panel of the instrument The green LED on the front will illuminate indicating that the system is ready and to confirm that power is being supplied and all the internal light modules are functioning properly The start up initialization process takes approximately 30 seconds After this time has elapsed the host computer can be turned on At this time you can also power up the power supply or CEU if you have a VersaDoc 3000 or 5000 system Note If the LED indicator fails to illuminate and the instrument is inoperative check that all power cables are firmly attached and that power is being supplied to the unit If the unit still remains inoperati
39. in DIN connector is for the VersaDoc 1000 and 4000 cameras and the cable with a 15 pin DIN for the VersaDoc 3000 See Figure 3 2 NOTE VersaDoc 3000 systems with Enclosures that are serialnumber XXXBR 300 or greater come with a separate power supply for the camera This power supply already includes a power cable for the VersaDoc 3000 camera VersaDoc 3000 systems Connect this cable between the camera power socket on the camera module and the enclosure Picture shown below is for enclosures with serial numbers below XXXBR0300 VersaDoc 1000 and 4000 Camera Power Connector VersaDoc 3000 Camera Power connector 9 pin camera power connector on top side of the rear panel 15 pin camera power connector on top side f the rear panel User s Manual e 3 6 If your enclosure has a serial number above XXXBR300 then connection should be made per pictures shown below VersaDoc 1000 and 4000 VersaDoc 3000 Camera Power Camera Power Connector connector Camera Power connector on Camera Power connector on the cable from camera power top side of the rear panel supply Figure 3 2 NOTE The VersaDoc 4000 camera must be connected to the same power port as the VersaDoc 1000 Connecting the AIA CABLE For VersaDoc 1000 and 3000 and 4000 only 1 Connect the AIA cable Part 800 0247 to the AIA port on the camera See Figure 3 4 Push the cable to the connector such tha
40. 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 Green SYBR Gold Radiant Red SYPRO Orange SYPRO Red 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 amp 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 e 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 Seri
41. kground removed from glass plate Thin polyacrylamide samples can be transferred to exposed x ray film and imaged using UV epi mode 660 NM filter is not in place Install 660 NM filter onto lens Verify reselect correct application Light leak Check for light leaks ensure Camera Module tightly connected to Use low fluorescence agarose used Remove sample and acquire a control image Destain if appropriate was Increase destain insufficient turn housing obstruction obstruction assistance Bad filter wheel cable or connection Poorly seated lamps Turn the lamps in the sockets to make sure lamps are seated properly in their sockets Epi lamps are not turning Bad lamps Replace lamps on Door interlock not working Contact Bio Rad with age acquire image has the image increased Verify application is correct for sample Poor Sample may have degraded Some Chemi samples have a chemiluminescence short lifetime make sure the sensitivity sample is hot and fresh Incorrect lens filter used Use the 50 mm high NA lens for best chemi results and use no filter Position 5 or higher Sample on platen with chemi Place sample on chemi tray or tray installed remove tray from sample chamber Incorrect f stop setting Adjust f stop to a lower value esi aca a f 1 4 recommended The 660IR cutoff filter was not Remove 660 cutoff filter E T a teers ree time e eee User s Manual e 6 2 Software Troubleshooting In case you installed the c
42. lace or repair the defective parts free of charge For the exact terms of warranty please see the Instrument Warranty Card In the event that the VersaDoc must be returned to the factory for repair under warranty the instrument must be packed and returned in its original shipping container Bio Rad shall not be liable for any incidental special or consequential loss damage or expense directly or indirectly arising from use of the VersaDoc system Bio Rad makes no warranty whatsoever in regard to products or parts furnished by third parties such being subject to the warranty of their respective manufacturers Service under this warranty shall be requested by contacting your nearest Bio Rad office This warranty does not extend to any instruments or parts thereof that have been subject to misuse neglect or accident or that have been modified or serviced by anyone other than Bio Rad or its representative or that have been used in violation of Bio Rad instructions It also does not extend to instruments or parts thereof that have been used with fittings or other spare parts not authorized by Bio Rad Laboratories that are interfaced to inappropriate external devices that have been exposed to inappropriate solvents cleaning agents or samples The warranty also does not cover instrument damage resulting from facility problems such as power surges The foregoing obligations are in lieu of all other obligations and liabilities including neglig
43. m re boots and Windows 2000 XP starts it will find the PCI card and go through a FOUND NEW HARDWARE installation routine and find the drivers that were just installed NOTE In case the PCI card was installed before the software then go to section 6 for software troubleshooting In case of the MAC systems it does not matter if the PCI Card is installed before or after installing the software and drivers Mac based VersaDoc systems NOTE This procedure applies to both Mac OS 9 xx and OS 10 xx based systems h Insert The Discovery Series software CD into the CD ROM drive of the MAC Installer will open and offer choices User s Manual e 3 17 j Quantity One Installer Easy Install 2j This will install Quantity One To also install drivers for an imaging device choose Custom Install from the popup menu m Install Location ems will be installed in the folder Applications Mac 0S 9 on the disk untitled Install Location untitled Choose custom install from the pulldown menu in this window and click on INSTALL The following window will open Quantity Che Installer HE Custom install E EJ Quantity One Pd Users Guide 1 Gel Doc EQ ChemiDoc EQ Drivers O ChemiDoc XRS Drivers EJ VersaDoc Drivers Disk space available 2 844 496K Approximate disk space needed 34 960K Install
44. nvironment it is recommended that all emission filters are stored in a sealed container with desiccant User s Manual e 5 5 Section 6 Troubleshooting amp Technical Information 6 1 Problem Solving Guide Problem Possible Cause Solution VersaDoc is not Power is not supplied or the Ensure power is supplied to the responding to host system and that the switch is computer turned on connected properly and ensure it is seated properly connected properly connected and seated properly digitizing card is connected ee ee ee Startup sequence is incorrect restart in opposite sequence Computer has a conflicting Contact Bio Rad for assistance program or initiation init file Image is not visible on The Transform function in the Set to a lower maximum value the monitor or only low software is set too high signal counts are detected Lens cap is covering lens Remove lens cap Insufficient integration time Integrate sample for a longer time imaging nonchemi sample chamber application Wrong imaging area selected Verify reselect correct area Bad lamp Replace lamp are clean across the image not working spots sample platen or optics White light Image has Chemi Sample tray was not Use the Chemi Sample tray on vertical lines used the UV Filter platen and reacquire the image User s Manual e 6 1 Problem Possible Cause Solution Fluorescent image has Image was taken without being Remove plate from sample high bac
45. om the sample to the CCD As such the longer the exposure time the brighter the captured image will be For high intensity applications including colorimetric and high intensity fluorescence experiments an exposure time of only a few seconds is typically required For low intensity applications such as chemiluminescence an exposure time of several minutes may be required The exposure period required to produce an optimal image varies considerably and may need to be optimized for your particular sample Typical exposure conditions for different sample types have been included in Table 4 1 as a guide to selecting a suitable exposure time This table also indicates the preferred lens for the sample and if any accessories are recommended Table 4 1 Recommended exposure times and setup Sample Recommended Lens amp Accessories Exposure Filter Used Fluorescent Stain Gel 3 30 sec Zoom IR None Fluorescence End Label 30sec 5 min Zoom IR None Gel Chemifluorescent Blot 0 5 5 sec Zoom IR None Colorimetric Gel 0 1 1 sec Zoom IR VersaDoc white light conversion screen X ray film 0 1 1 sec Zoom IR VersaDoc white light conversion screen Weak 5 10 min 50 mm Sample Chemi Tray if Chemiluminescence sample is small Strong 10 sec 2 min 50 mm Sample Chemi Tray if Chemiluminescence sample is small User s Manual e 4 6 4 3 9 Acquiring the Image To collect the sample image simply press the ACQUIRE button The yellow LED on the front pan
46. on layers comprising the CCD Dark current noise is the square root of the number of dark current electrons The presence of dark current is an additional concern in low light level applications It is important to ensure that dark current noise does not exceed read noise from the signal even when long integration times are used Signal to Noise Signal to noise ratio SNR is the measure of the signal quality at a given pixel It is the ratio of the measured signal to the overall measured noise at that pixel Dynamic Range Dynamic range of a CCD is simply defined as the ratio of CCD saturation to the read noise It is the ability to quantitatively detect very dim and very bright pixels within a single image Quantum Quantum efficiency is the measure of the effectiveness of an imaging Efficiency device to produce electronic charge from incident photons This is an especially important property when performing very low light level imaging Dead Pixels There are a variety of different grades of CCD chips Each grade has some percentage of dead or bad pixels These are typically displayed as white or dark lines on the image Most CCD systems correct for dead pixels Image Image resolution refers to the spacing of pixels in the image and is Resolution measured in pixels per inch ppi If an image has a resolution of 72 ppi this means that it contains 5182 pixels 72 x 72 in a square inch Monitor Monitor resolution defines the number of dot
47. or captive screw on the EPI UV Slots for EPI UV module Figure 3 14b Figure 3 14c 6 Next attach the epi white module to the epi UV module by locking in the tongue and groove located at the outer top edges of each module See figure 3 14c 7 Now secure the epi white module to the epi UV module using the latch and screw mechanism located at the front plate of the modules See Figure 3 15 Figure 3 15 8 Next connect the cable from the epi white module to the appropriate connector on the ballast assembly 9 Re install the access panel to the ballast panel NOTE The plugs for each illumination module are keyed and cannot be interchanged Each plug will snap together only to the appropriate socket 3 2 7 Electrical and Communication Connections Power The power entry module of the VersaDoc system is configured for operation at 100 120 VAC 60 Hz or 220 260 VAC 50 Hz After checking that the system s power switch is turned off insert an approved power cord into the power entry module located on the bottom right of rear panel of the unit See Figure 3 16 User s Manual e 3 13 Warning This instrument must be connected to an appropriate AC voltage mains 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 7 ED Power entry module at the Power entry modul
48. orrectly 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 e 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
49. ot 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 e 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 1 510 741 5802 email Isg techserv us bio rad com For service or technical support Toll free 1 800 424 6723 Fax 1 510 741 5802 For information concerning Bio Rad Laboratories and its products visit our Worldwide Web site at http www bio rad com User s Manual e 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 th
50. pany and Bio Rad manufacturing The Quantity One acquisition and analysis software is supplied in a separate box User s Manual e 3 3 The VersaDoc hardware should arrive complete with the following items eE Tati ay 1 Item VersaDoc light tight enclosure Photo VersaDoc camera module Shown Model 1000 camera module model 3000 4000 and 5000 are shown later in this section VersaDoc transilluminator module already installed inside the light tight enclosure Pair of UV epiilluminator modules Pair of White epi illuminator Modules Sample chemi tray Camera power cable VersaDoc 1000 and 4000 only Or Fan assembly power cable VersaDoc 5000 only Camera AIA interface cable Serial USB communication cable 00 RINNAN G User s Manual e 3 4 Quantity Item Sample Holder Kit VersaDoc Fluorescent Reference Plate PCI Digitizing Card White Light Conversion Screen Optional Filters 530DF70 520LP 610LP Clear 660Cutoff Lenses 20 40mm Zoom 50mm Fixed Lenses 28 80mm Zoom 50mm Fixed Lens and Filter Cleaning Kit Focusing Target Power Cord Instruction Manual Camera Specification File CD 58mm 52mm Step Down Ring 3 NINI S S S Se Warranty Card These are provided with VersaDoc 1000 model only These are provided with VersaDoc 30
51. pt you to remove the sample NOTE Please make sure that the surface of the VersaDoc white light conversion screen is clean after the sample has been removed After the image has been acquired its appearance can be optimized The image may also be analyzed in various ways using the Quantity One program Analysis options include object volume analysis lane profile analysis including regression analysis and molecular weight determination colony counting fingerprinting VNTR and differential display studies The image and various data reports may also be printed or exported to other software programs Please refer to the Quantity One software manual for detailed instructions Note Please refer to the Quantity One software manual for information concerning additional features available in the acquisition window for VersaDoc User s Manual 4 7 Section 5 Care and Maintenance 5 1 General Maintenance With regular use the VersaDoc system should provide years of trouble free operation without any need for regular operator maintenance other than cleaning If you suspect that the VersaDoc requires servicing please contact your local Bio Rad office The outside surface of the VersaDoc should be periodically cleaned with water mild liquid soap and a sponge or soft cloth towel Caution Never use abrasive cleaners solvent based cleaners alcohol or scouring pads to clean the external surface of the instrument Caution Always disconnect the Versa
52. red 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 1 510 741 5802 email Isg techserv us bio rad com For service or technical assistance Toll free 1 800 424 6723 Fax 1 510 741 5802 For information concerning Bio Rad Laboratories and its products visit our Worldwide Web site at http www bio rad com 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 Cam
53. ribute to background signal Sample Chemi Tray It is recommended that the Sample Chemi tray Figure 4 2 be used for all small chemiluminescence samples 8 x 8 cm or less This tray slides onto the guides on the each epi illumination assembly and allows the sample to be placed closer to the camera Large chemi samples should be imaged on the platen To insert and remove the chemi tray the door to the enclosure must be fully opened Note When using the VersaDoc for non chemiluminescence applications the sample tray should be removed from the enclosure as it will block sample signal from reaching the CCD camera When using white light epi illumination the sample tray should be placed on the dark reflective platen of the transilluminator to avoid unwanted reflections on your image User s Manual 4 3 Fig 4 2 VersaDoc chemi sample tray 4 3 4 Lens Selection and Setup The VersaDoc system is supplied with two standard lenses a flexible Zoom lens and a high numerical aperture 50 mm lens with improved collection efficiency For optimal image acquisition it is recommended that the zoom lens with 660 nm cut off filter installed be used for all fluorescence and colorimetric applications This lens can also be used for high intensity chemiluminescence experiments however it is not ideal for this type of application For the best chemiluminescence results it is recommended that the 50 mm fixed lens with no cut off filter be us
54. s 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 lt xxxx gt 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 c
55. s Use Recommendation For optimal image acquisition it is recommended that the zoom lens with 660 nm cut off filter installed is used for all fluorescence and colorimetric applications In chemiluminescence experiments the 50 mm fixed lens with no cut off filter is recommended Zoom Lens Installation To correctly install the zoom lens Follow the procedure outlined below Figure 3 20 1 Remove the lens from its packaging and retain the packaging for future storage 2 Remove the front lens cap and install the 58mm 52mm step down ring then the 660 short pass SP filter onto the lens User s Manual e 3 23 3 Remove the protective cover from the lens mount rear of lens and check that the lens is clean If the lens is dirty it should be cleaned with the materials provided in the lens and filter cleaning kit 4 Open the door to the main door and position the lens so that the white line on its mount matches the white mark on the base right hand side of the camera assembly 5 Insert the mount of the lens into the base of the camera assembly and turn the lens counter clockwise to the left until you hear it click The white mark and setting indicators on the lens should now be directly in front of you 6 The lens in now locked into position and the lens cap and protective platen cover can be removed Figure 3 20 Steps in zoom lens installation High Sensitivity 50 mm Lens Installation To correctly install the 50 mm
56. s or pixels per unit length of Resolution output It is commonly measured in dots per inch dpi The monitor resolution determines the size of the displayed image and should not be confused with image resolution which reflects the spacing of pixels in the image User s Manual e 6 7 6 6 Spare Parts List Part Number Description 8000247 Cable Camera AIA 9210780 Cable Camera DC Power VersaDoc 1000 9310070 Cable Serial PC DB9M 9310071 Cable USB Type A to B 9310072 Cable Serial MAC DIN8 TO DB9M 9000213 Lamp EPI White Light 9000217 Lamp UV EPI Transilluminator 9204929 UV Filter glass for EPI UV 9210491 Diffuser plastic for Epi white module 8000229 EPI UV Module Left 8000230 EPI UV Module Right 8000231 EPI WHITE Module Left 8000232 EPI WHITE Module Right 8000242 Transilluminator top cover with UV filter glass 8005363 Kit Focusing Target 4100167 Filter Order Form 9210640 Plate Reference Fluorescent 1002363 Shipping Container Complete System 1002364 Shipping Container Enclosure Only You will need these in pairs Other Useful Part Numbers Part Number Description User s Manual e 6 8 Life Science Group 4000183 REV E Bio Rad Laboratories Web site www bio rad com Bio Rad Laboratories Main Office 2000 Alfred Nobel Drive Hercules CA 94547 Ph 510 741 1000 Fx 510 741 5800 Also in Australia Ph 02 9914 2800 Fx 02 9914 2889 Au
57. sition window The following window will open on the screen Note If the computer cannot establish communications with the VersaDoc a message will indicate this and give the user the option of entering a simulation mode E Quantity One MCE Ele Ed View mage Lane Bard Mach Vome gnajsa Bepets Window Help gt da AGL Step Select Appkcadon of aredi Oord Oad Channel 4 sea Fiworescein 5200770 UV TRENS 4 Gain ixl Bin Poson Step Ill Sat Expose Tene Et Opener kJ Optionse Uritomnty Omare O Optimise Eposu Dagta Oston _ Haghight Saturated Prois insg fle sce 3 00 Md Opten Drew Expocwe State m Figure 4 1 VersaDoc acquisition screen in Quantity One User s Manual e 4 2 4 3 2 Selecting the Application The Quantity One program uses an application oriented format to simplify user selection of collection parameters To correctly set the parameters for collection simply click the SELECT button in Step Figure 4 1 and identify the application name matching your sample type For detailed acquisition instructions please refer to the Quantity One software instruction manual 4 3 3 Placing Samples in the Imaging Chamber The VersaDoc can accommodate a variety of sample types and sizes The sample stage is 25 X 25 cm This configuration supports the acquisition of smaller areas of interest within very large samples The imaging area is liquid sealed so wet samples may be placed
58. stem User s Manual e 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 non uniformities 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 transillumin
59. stria Ph 01 877 89 01 Fx 01 876 56 29 Belgium Ph 09 385 55 11 Fx 09 385 65 54 Brazil Ph 55 21507 6191 Canada Ph 905 712 2771 Fx 905 712 2990 China Ph 86 10 8201 1366 68 Fx 86 10 8201 1367 Denmark Ph 45 44 52 1000 Fx 45 4452 1001 Finland Ph 358 0 9 804 2200 Fx 358 0 9 804 1100 France Ph 01 47 95 69 65 Fx 01 47 41 9133 Germany Ph 089 318 84 177 Fx 089 318 84 123 Hong Kong Ph 852 2789 3300 Fx 852 2789 1257 India Ph 91 124 6398112 113 114 Fx 91 124 6398115 Israel Ph 03 951 4124 Fx 03 951 4129 Italy Ph 34 91 590 5200 Fx 34 91 590 5211 J apan Ph 03 5811 6270 Fx 03 5811 6272 Korea Ph 82 2 3473 4460 Fx 82 2 3472 7003 Latin America Ph 305 894 5950 Fx 305 894 5960 Mexico Ph 52 5 534 2552 to 54 Fx 5255245971 The Netherlands Ph 0318 540666 Fx 0318 542216 New Zealand Ph 64 9 4152280 Fx 64 9 443 3097 Norway Ph 47 23 38 41 30 Fx 47 23 38 41 39 Russia Ph 7 095 979 98 00 Fx 7 095 979 98 56 Singapore Ph 65 2729877 Fx 65 2734835 Spain Ph 34 91 590 5200 Fx 34 91 590 5211 Sweden Ph 46 0 8 55 51 27 00 Fx 46 0 8 55 51 27 80 Switzerland Ph 061 717 9555 Fx 061 717 9550 United Kingdom Ph 0800 181134 Fx 01442 259118
60. t it clicks and snaps in place properly AIA CONNECTORS ON EACH END OF THE CABLE VERSADOC 1000 4000 VERSADOC 3000 CAMERA CAMERA AIA CONNECTOR AIA CONNECTOR Figure 3 4 User s Manual e 3 7 2 The other end of the AIA cable will be connected to the PCI digitizing card that will be installed in the PC after software installation as shown later in this procedure NOTE The steps describing the installation procedure for the PCI digitizing card follows later in this procedure 3 2 5 Installing VersaDoc 5000 Connecting the cables to the camera module 1 The VersaDoc 5000 camera module comes with a camera controller unit CEU and a controller cable See figure 3 6 below Camera Module Camera Controller Unit CEU 3 Camera Controller Cable Figure 3 6 2 Couple the VersaDoc 5000 camera module to the enclosure as shown in the section 3 2 3 above See Figure 3 1 for details 3 Next connect the CEU to the camera Caution The default voltage setting on the camera power supply module is 120 VAC You must follow the instructions below to make sure proper voltage selection is made and fuse is used for you AC voltage environment Caution The VersaDoc 5000 camera module has a BLUE plug installed on the connector on the camera This plug must not be removed until the module is installed to the enclosure and the camera controller unit is ready to be connected to the Camera Se
61. the hole indicating the selected voltage 230 VOLT and arrow must point inward Insert the board back into the socket with the letters facina the riaht side NOTCH on each side of the PCB 230 Volt setting Figure 3 10b 6 Now reinstall the tiny PCB back into it s socket such that the numbers on it face towards the right side towards the Fuse holder inlet 7 Next remove the Phillips screw that holds the fuse holder and turn the holder around so that the two 1 amp fuses face towards the socket See Figure 3 11 User s Manual e 3 10 Figure 3 11 8 Push the tab until it locks in its socket 9 Check again to make sure that the plastic stub indicates the desired voltage selection Connecting the VersaDoc 5000 Camera and CEU Cables 3 4 Connect the AIA cable to the connector labeled AIA on the CEU connector panel The other end of this cable will be connected to the PCI digitizing card in your PC Remove the BLUE shorting plug from the camera and connect the camera control cable between the camera and the CEU See figure 3 12 Fan Assembly Power Connector Blue Shorting Plug VesaDoc 5000 Camera Module Blue Shorting plug Figure 3 12 Connect the AC power cord to the AC inlet on the CEU but do not power up the CEU yet For units serial number below XXXBR300 Connect the fan power cable from the fan assembly 5000 models only to the DB9 power
62. tting the VersaDoc 5000 System Power Supply Voltage If required 1 Familiarize yourself with the camera controller unit CEU See Figures 3 7a b and c below User s Manual e 3 8 Camera Controller Cable Connector Figure 3 7c 2 A small white tab on the AC inlet located on the rear panel indicates the voltage setting on your camera controller unit See Figure 3 8 Insert a small screw driver and pull out the tab White plastic stub shows the current voltage setting Make sure it matches with the local voltage Figure 3 8 3 Pull out the small tab near the AC inlet using a small screwdriver See Figure 3 8 4 The TAB holds a fuse completely remove it This will expose a tiny PCB located in a tiny slot as shown in Figure 3 9 User s Manual e 3 9 Small PCB in a tiny slot This side of the PCB has letters on this side Figure 3 9 5 Using the plastic stub on the PCB select the orientation of the board so that the desired voltage numbers and arrow point towards the socket for the board The tab on the inside surface of the stub must match with the notch on the tiny PCB See Figure 3 10a and 3 10b Plastic stub that shows through the hole indicating the selected voltage 100 VOLT and arrow must point inward Insert the board back into the socket with the letters facing the right side Setting for 100 volt operation Figure 3 10 a Plastic stub that shows through
63. ve or the VersaDoc acquisition window cannot be opened on the host computer please contact the Bio Rad Technical Service Department for assistance The VersaDoc should be switched on at least 30 seconds before the host computer to allow for complete initialization If the VersaDoc is not fully operational before the computer is turned on the system will not be recognized as an attached Serial USB device and the camera may not be recognized by the digitizing card thus you will not be able to communicate with the VersaDoc from the Quantity One acquisition window For best imaging results it is recommended that the VersaDoc be allowed to warm up for 10 minutes before use 4 2 Overview of Operational Steps The user will typically complete the following series of steps when acquiring an image using the VersaDoc 1 Start the program and open the acquisition window 2 Select the desired application 3 Place the sample on transilluminator platen converter screen or chemi tray as the case may be and optimize its position Focus Adjust the lens aperture and zoom Readjust focus if required Select the exposure acquisition time Acquire the image ONO User s Manual 4 1 4 3 Detailed Operating Procedures 4 3 1 Opening the Acquisition Window After starting your computer open the Quantity One acquisition and analysis program by double clicking on the Quantity One icon From the FILE menu select VERSADOC to open the instruments acqui
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