BioDocAnalyze (BDA) digital - Biometra

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BioDocAnalyze (BDA) digital - Biometra

Gel Documentation SystemBioDocAnalyze (BDA) digitalOrder Numbers034-000, 034-006, 034-050, 034-056,034-302, 034-312, 034-303, 034-313034-306, 034-316Instructions for InstallationandImage AcquisitionSoftware Version 2.66.3.409-990-017/englishVersion 02_12Please read the operating instructions carefullybefore using the system!Biometra GmbHD-37079 Göttingen ServiceRudolf-Wissell-Straße 30 Rudolf-Wissell-Str. 14-16D-37079 Göttingen D-37079 GöttingenTel.: +49 551 50686-0 Tel.: +49 551 50881-10/12Fax: +49 551 50686-66 Fax: +49 551 50881-11e-mail: Info@biometra.com Service@biometra.cominternet: http://www.biometra.de


2All rights reserved. No part of this publication may be reproduced, stored in a retrieval system,or transmitted, in any form or by any means without the prior written permission of BiometraGmbH nor be otherwise circulated electonically or in print.In no event Biometra GmbH shall be liable for indirect, incidential or consequential damagesresulting from the use of the information supplied by this manual. This manual was writtenwith due care and Biometra GmbH shall not be liable for any fault or omission.November 2012.Tradenames of software or hardware cited herein, esp. those of the Microsoft Corp., are registered,patented or protected by other legal means.BDAdigital Manual, Vers. 02_12


Contents3Contents1 INSTALLATION OF BDADIGITAL...................................................................................................41.1 COMPONENTS ..............................................................................................................................41.2 ASSEMBLY ...................................................................................................................................41.2.1 Personal computer and monitor..........................................................................................41.2.2 Copy protection (Dongle, Hardlock)....................................................................................41.2.3 Set up of single lens reflex camera.....................................................................................51.2.4 Bandpass Filter...................................................................................................................71.2.5 Filter wheel labels ...............................................................................................................81.2.6 Mounting the camera at BDA Hood....................................................................................81.2.7 Mounting the camera at BDA Box 1/2/3 .......................................................................... 101.2.8 Darkhood, transilluminator and converter plate............................................................... 111.2.9 Thermal printer................................................................................................................. 111.3 INSTALLATION OF THE SOFTWARE .............................................................................................. 121.3.1 Overview .......................................................................................................................... 121.3.2 Installation of the Camera Canon EOS 1100D (optional)................................................ 131.3.3 Installation of the BioDocAnalyze Program ..................................................................... 141.3.4 Installation of Thermal Printer Mitsubishi P95DE ............................................................ 152 START OF THE PROGRAM ......................................................................................................... 152.1 CHOICE OF MAIN WINDOWS ........................................................................................................ 163 BDADIGITAL IMAGE CAPTURE WITH SINGLE LENS REFLEX CAMERA, E.G. EOS 1100D. 173.1 THE IMAGE CAPTURE................................................................................................................. 183.2 FUNCTIONS AND CAPTURE PARAMETERS.................................................................................... 193.2.1 Profiles with Capture Parameters.................................................................................... 193.2.2 The Card „Settings“ ......................................................................................................... 203.2.3 Camera Settings for Typical Gels.................................................................................... 213.2.4 Further Functions for Image Capture............................................................................... 223.2.5 Take photo and display settings ...................................................................................... 233.2.6 Basic functions................................................................................................................. 253.2.7 The Gel Picture Window .................................................................................................. 254 BDADIGITAL IMAGE CAPTURE WITH DIG. COMPACT CAMERA, E.G. POWERSHOT G10 .264.1 THE IMAGE CAPTURE................................................................................................................. 274.2 FUNCTIONS AND CAPTURE PARAMETERS.................................................................................... 284.2.1 Profiles with Capture Parameters.................................................................................... 284.2.2 The Card „Settings“ ......................................................................................................... 284.2.3 The Card „Advanced“ ...................................................................................................... 304.2.4 Camera Settings for Typical Gels.................................................................................... 314.2.5 Further Functions for Image Capture............................................................................... 324.2.6 Take photo and display settings ...................................................................................... 334.2.7 Basic functions................................................................................................................. 344.2.8 The Gel Picture Window .................................................................................................. 345 SERVICE........................................................................................................................................ 356 EQUIPMENT DECONTAMINATION CERTIFICATE .................................................................... 367 DISPOSAL ..................................................................................................................................... 38BDAdigital Manual, Vers. 02_12


4Installation1 Installation of BDAdigitalconcerning034-000 BDAdigital core set, 034-006 BDAdigital core set BL034-050 BDAdigital compact , 034-056 BDAdigital compact BL034-302, 034-312 BDAdigital System 20034-303, 034-313 BDAdigital System 30034-306, 034-316 BDAdigital System BL1.1 ComponentsThe system comes with:- BDA software (CD-ROM) and manual- Dongle (copy protection key, hardlock)- Digital camera inclusive power supply- Bandpass filter BP595 for EtBr stained gels (not in sets “BL”)Additionally with BDAdigital compact:- Darkhood BDA Hood incl. anti-theft camera mountingAdditionally with BDAdigital System 20, BDAdigital System 30, BDAdigital System BL:- Darkhood BDA Box 2 incl. anti-theft camera mounting- Transilluminator UVstar 20 resp. UVstar 30 resp. BLstar 16- UV converter plate (not in System “BL”)- Thermal printer incl. USB cable- TFT monitor- Personal computer, installed1.2 Assembly1.2.1 Personal computer and monitorAttach the cable of the monitor to the VGA port of the graphic card of the PC.Connect also mouse and keyboard to the computer. Connect monitor and PC via cable withthe appropriate power supply system.Compatible operational systems: Windows XP and Windows 71.2.2 Copy protection (Dongle, Hardlock)The BioDocAnalyze software is protected by a copy protection key (dongle, hardlock).Note: The dongle is the software licence.The dongle is supplied as key for the USB port of the computer.This dongle is plugged to the USB port of the computer.After installation the dongle is automatically detected and flashes inred.BDAdigital Manual, Vers. 02_12


1.2.3 Set up of single lens reflex cameraThe following instructions focus to the basic installation steps.5InstallationPlease also refer to the camera instruction manual supplied on the CD-ROM with the Canoncamera.1.2.3.1 Attaching the lens to the cameraRemove the caps.Remove the rear lens cap and thebody cap by turning them as shownby the arrows.Attach the lens.Align the lens’ red or white index withthe camera’s index matching thesame color. Turn the lens as shownby the arrow until it snaps in place.On the lens, set the focus modeswitch to (autofocus).If it is set to (manual focus),autofocus will not operate.Remove the front lens cap.Note:Minimizing Dust• When changing lenses, do it in a place with minimal dust.• When storing the camera without a lens attached, be sure to attach the body cap to thecamera.• Remove dust on the body cap before attaching it.BDAdigital Manual, Vers. 02_12


6Installation1.2.3.2 Attaching the power supply to the cameraConnect the power cord.Connect the power cord as shown in the figure.Connect the DC Coupler.Connect the DC cord´s plug to the DC Coupler.Insert the DC Coupler.Open the camera´s battery compartment cover slidingthe lever. Insert the DC Coupler until it locks in place.Push in the DC cord.Open the DC cord groove cover and install the cord asshown.Close the camera´s battery compartment cover.BDAdigital Manual, Vers. 02_12


7Installation1.2.3.3 Attaching the USB to the cameraNote:In case that you also want to use the Canon software included in the camera delivery forother applications independend from BDAdigital please install the Canon software before youconnect the camera to the computer!The Canon software is not required for running the camera under BDAdigital.Open the terminal cover and connect the USB cableto the USB.Connect the other side of the USB cable to the USBport of the computer.Note:To avoid any hardware detection problems it is highlyrecommended to connect a USB device always to thesame terminal of the computer where it was initiallyinstalled.1.2.4 Bandpass FilterStandard delivery is a red bandpass filter with transmission maximum of 590 nm for the typicallyused fluorescent stain ethidium bromide. For other stains please request for applicableoptional filters. For applications with a blue light illuminator BLstar no bandpass filter isneeded.1.2.4.1 With small darkhood BDA Hood of BDAdigital compact, BDA Box 1 or a stand:Please screw the bandpass filter directly to the camera zoom lens.For image acquisition of coloured samples, e.g. silver or Coomassie Blue stained gels, illuminatedwith white light no bandpass filter is needed.1.2.4.2 With Darkhood BDA Box 2 or BDA Box 3:Please insert the bandpass filter into the filter wheel: Open the darkhood sliding door andopen the UV protection shield up to a horizontal position. Slowly pull out the filter wheel withthe knob inside the darkhood, below the filter wheel. The filter wheel is slided out and thefilter can be inserted into the wheel. Please choose the wheel position which is opposite tothe corresponding filter label (see 1.2.5).Note:Filters with slightly higher filter holder shall be inserted in borehole Nr. 3 of the filterwheel. Then Nr. 1 is seen at filter wheel front.BDAdigital Manual, Vers. 02_12


8Installation1.2.5 Filter wheel labelsDelivery of a BDA Box includes several small filter wheel labels.These labels can be applied to darkhoods with filter wheel (BDA Box 2, BDA Box 3) at thefront panel of the filter wheel. Please note that the visible front position number correspondsto the opposite filter wheel position. The standard delivery of BDA systems includes the red„590 nm/ethidium bromide filter“.The green „520 nm/SYBR Green filter“ and also the yellow wide pass filter with transmissionrange of 490 nm up to 690 nm can be bought as optional components.1.2.6 Mounting the camera at BDA Hoodin BDAdigital compact sets1. Mounting of cameraCamera incl. zoomlens and screwedbandpass filterHexagon socketfor screwing the camerato the bracket.Light trapCamera bracket.By slight release fthe two knurledhead screws thebracket can bemoved forwardand backward aswell as left andright for straightalignment of thecamera (pleasecheck by manualzooming that noresistance ornoise is noted!).BDAdigital Manual, Vers. 02_12


9Installation2. Covering of lens releaseSpecial screwCover for lens releasebutton.Please push the pinthrough the left slot andslide the cover up towardsthe camera.Specialscrew driver3. Security bracketSpecialscrew driverSpecial screwsSecurity bracketMounted cover forlens release buttonBDAdigital Manual, Vers. 02_12


10Installation1.2.7 Mounting the camera at BDA Box 1/2/31. Mounting of cameraCamera incl.zoom lens(with BDA Box 1:with screwedbandpass filter,without upperlight trap)Light trapsHexagon socketfor screwing the camerato the bracket.Camera bracket.By slight releaseof the two knurledhead screws thebracket can bemoved forwardand backward aswell as left andright for straightalignment of thecamera (pleasecheck by manualzooming that noresistance ornoise is noted!).2. Covering of lens releaseCover for lens releasebutton.Please push the pinthrough the left slot andslide the cover up towardsthe camera.Special screwSpecialscrew driverBDAdigital Manual, Vers. 02_12


12Installation1.3 Installation of the SoftwareBDAdigital software with software version no. 2.66.3.0 and higher is compatible withoperational systems Windows XP and Windows 7.The installation is only necessary in case you bought the sets 034-000 and 034-050without a computer from Biometra. If BioDocAnalyze comes with a Biometra computer,the software is completely installed and the system is ready to use after unpackingand installing the cables.PC minimum requirements: Personal computer with Windows XP or Windows 7, Intel ®Core TM i3 processor, 2.8 GHz or similar, graphic card 1280 x 1024, > 2 GB RAM, 3 USB2.0ports, CD-ROM drive.For installation it is necessary to work with system administrator rights.Software installation: This will take, depending on the computer and installation experience,between 15 and 45 minutes. In case of problems during or after installation, please contactthe Biometra BioDocAnalyze customers service, phone +49(0)551-5068612, fax +49(0)551-5088111, e-mail H.Becker@analytik-jena.de.1.3.1 Overview! For installation procedure please refer to following chapters with detailed information.completed1.3.1.1 Installation of camera (s. 1.3.2).......................................................................Installation of digital camera driver and image editing and processing programs from CanonCD-ROM (optional, not required for BDAdigital application)Afterwards connect camera to PC.1.3.1.2 Installation of BDA software incl. dongle (s. 1.3.3).......................................from BDA CD-ROM1.3.1.3 Installation of thermal printer (s. 1.3.4)..........................................................from BDA CD-ROMBDAdigital Manual, Vers. 02_12


13Installation1.3.2 Installation of the Camera Canon EOS 1100D (optional)! The camera driver from the Canon Digital Camera Solution CD must be installedbefore connecting the camera to the PC!1.3.2.1 Installation of the Canon programs1. Click [Easy Installation] to start installation.2. Follow the windows displayed for the rest of the installation procedure.3. When installation ends, the window with request for restart appears.4. Click [Restart].1.3.2.2 Basic camera settingsThe camera is not yet connected to the PC.1. To have correct dates on your pictures, the time and date in the cameras menue, cardsettings, must be set.2. Connect the camera with mains adapter with the power supply system.3. In control panel, energy options the standby mode of the computer and the switch offof the harddisk should be set to „never“ as after reactivation the connection to the cameramay be lost. Switching off the computer monitor after some minutes of inactivity or thescreen saver will not disturb the camera function.Afterwards connect the camera to the computer by its USB cable.! To avoid any Windows problems with the USB ports it is recommended to connectUSB devices to the same USB port as used for installation of the devices.Turning on the power The camera turns on. The camera turns off. Set to this position whennot using the camera.When the camera is connected to the computer the camera will automatically switch to thePC mode. The computer mostly will show a short note that the camera is detected. In casethat a window of Canon or Windows software is opened asking for the next action with thecamera please close this request.BDAdigital Manual, Vers. 02_12


14InstallationSetting the Shooting ModeChoose the mode “Manual Exposure” to be free to set both the shutter speed and the aperturemanually. This mode is recommended for use with BDAdigital.Set the Mode Dial to .1.3.3 Installation of the BioDocAnalyze Programincl. the driver for the copy protection key (hardlock, dongle)1. Insert the BioDocAnalyze installation CD into the PC drive. A window “Automatic replay”is opened. Choose “Open directory for display of files” or close the window and proceedwith 2.2. Start „my computer“ or the Windows Explorer and choose the CD-ROM drive.3. Start installation with double-click on the file „BDAdigital_setup.bat“ in the main directory.Now the drivers for the dongle and the BioDocAnalyze software are installed.4. Confirm the request for completing the installation.Note:Starting the BDAdigital image acquisition window for the first time you are asked totype in a 4-digit activation code to get free access to this software part. You will findthe requested code labeled to the copy protection key (see also section 3).********************************************************************It is also possible to install the BioDocAnalyze software and the drivers of the dongle separately:BioDocAnalyzesoftwareDongleStart the file „BioDocAnalyze_setup.exe“ in the directory“BDA\Release\Single” of the BioDocAnalyze CD and confirm allrequests.Start the file „hdd32.exe“ in the directory „HASP4_driver_setup”and confirm all requests.********************************************************************BDAdigital Manual, Vers. 02_12


BioDocAnalyze Software Update15InstallationWhen the BioDocAnalyze software shall be installed to an existing system as softwareupdate only the BioDocAnalyze software has to be installed newly.A new installation of other drivers and programs is not necessary.Installation:1. Please uninstall the existing BioDocAnalyze software versionby „Start, control panel, Software, BioDocAnalyze“ with the„delete“ button or alternativelyby “Start, All programs, Biometra, BioDocAnalyze, Uninstall BioDocAnalyze”.2. Now please install the BioDocAnalyze software from CD by double-click on the file„BioDocAnalyze_setup.exe“ in the directory “BDA\Release\Single” of theBioDocAnalyze CD.3. Confirm all requests.Restart your computer. Switch on the thermal printer before so you will be asked for theprinter driver installation automatically.1.3.4 Installation of Thermal Printer Mitsubishi P95DEThe default settings for printing in the configuration file biom1.ini of the BioDocAnalyze programare optimized for the thermal printer Mitsubishi P95DE with thermal paper KP65HM orKP95HG-CE and thermal printer Mitsubishi P93DW with thermal paper KP65HM orKP91HG-CE. In case another printer or another paper are used the printouts can be toodark. Then an individual adaptation of setting values (printcontrast, printbrightness, printgamma)in the biom1.ini is recommended.The printer drivers are on the BioDocAnalyze CD-ROM in the directory MitsubishiP9xx.Windows XP:The printer installation at the USB port runs widely automatically. Please confirm the differentrequests as recommended from the system as “standard installation”.Windows 7:The Mitsubishi printer P95DE is not automatically installed under Windows 7.Open “Start/Control panel/System and security/System/Device manager”. You will find “MitsubishiP95D” with question mark under “”Other devices”.Please double-click on “Mitsubishi P95D”, select “Driver” and afterwards “Refresh driver”.Browse to the BDA-CDROM in the computer CD/DVD drive for printer drivers. Now theprinter will be installed automatically.“The driver software was installed successfully” is displayed. Now the printer is displayed asstandard printer unter “Printer and fax machine”.Paper save modeA possibility to use the thermal paper more efficiently is to activate the paper save mode inthe printer settings:Choose „Start, settings, printer & fax“ and open the dialog box of the thermal printer. Choosecard „settings“ and set the paper save mode to „on“.BDAdigital Manual, Vers. 02_12


16Start of Program2 Start of the ProgramThe program is started from the desktop by a LEFT MOUSE BUTTON DOUBLECLICK on to theicon "BioDocAnalyze" or alternatively the command sequence "Start, Programs, Biometra,BioDocAnalyze".The BioDocAnalyze-Logo is opened and after several seconds displaced by the full framewindow "BioDocAnalyze" with a menu bar and a function bar.2.1 Choice of main windowsThe desired function is activated by click on theicon in the function bar.You have the choice between:Image capture with digital CCD camera (BDA live)Image capture with CCD video camera (BDAvideo)Image capture with digital single reflex camera (DSLR BDAdigital)Image capture with digital compact camera (BDAdigital)Gel analysis.This manual only refers to the image capture with the digital camera.Gel analysis is described in the separate manual „BioDocAnalyze“.BDAdigital Manual, Vers. 02_12


3 BDAdigital Image Capturewith Single Lens Reflex Camera, e.g.EOS 1100D17Image Capture DSLRPlease turn the camera on.The BDAdigital image capture software is started with a LEFT MOUSE BUT-TON CLICK on the icon „DSLR BDAdigital”.! When starting the BDAdigital capture softwarefor the first time after installation you will beasked for a 4-digit software code to activatethe capture screen.The code comes along with the dongle.The window „Capture digital camera“ is opened and shows the detected camera in line“Camera”.Fig. 3-1Window „Capture digital camera“BDAdigital Manual, Vers. 02_12


18Image Capture DSLRCameraIn case that in line “Camera” only „Model“ is shown the camera is not correctly installed ornot switched on. Please check and correct. Close the BDAdigital window and reopen again.ProfileWhen the capture window is opened it starts with the camera settings of the last opened profile.Shooting ModeWhen the mode dial of the camera was correctly set to (see chapter 1.3.2.2) the line“Shooting Mode” will accordingly display “M” for manual mode.3.1 The Image CaptureThese are the typical steps for image capture:1. Turn on the live preview: .2. Place the electrophoresis gel on the transilluminator.3. Turn on the light source of the darkhood.4. Straighten the gel with the help of the live preview in the transilluminator center.5. Choose the desired zoom area: Turn the zoom ring on thelens with your fingers.6. Choose the appropriate settings profile:7. Take a photo:The select box „AF“ is selected as default. As long as it is activated the camera will beautomatically focussing before taking the picture.Note: The focus mode switch of the lens must be set to ”AF”.If it is set to “MF” (manual focus) autofocus will notoperate.BDAdigital Manual, Vers. 02_12


8. If necessary optimize the exposuretime Tv and the lens aperture Av inwindow „Settings“. Then take anotherphoto.19Image Capture DSLRNote: These parameters can only be set in program mode “M” (manual).!Please consider: During image acquisition the live preview meantime is turned off asthe camera is not providing preview data at the same time. After finishing the imageacquisition the live preview is automatically shown again.Please don´t start any further functions of the BDAdigital software while the camera istaking the image which may take some seconds.9. Save and print the image:For details please see section 3.2.3.2 Functions and Capture ParametersThe window „Capture digital camera“ is widely self-explaining and very similar to generalknown parameters in photography. In spite of that the individual functions are explained inthe following.3.2.1 Profiles with Capture ParametersProfileSaveClearThis includes some profiles with working parameters for the image acquisition ofcertain gel types.A mouse click on the profile will set the parameters in the camera. The correspondingparameters are shown in the card “Settings”. It is essential that the ShootingMode is „manual“ otherwise the settings shown in the card Settings will not reallybe the used parameters.It is also possible to enter names for individual settings. After typing in the newname and setting the parameters the new profile has to be saved .Switch off of the „live image“ will accelerate the change of profiles.This saves user-defined profiles under the active profile name.Before saving you should check whether already a profile with the same name existsbecause it would be overwritten.This deletes the active profile. The Biometra saved profiles can not be deleted.BDAdigital Manual, Vers. 02_12


20Image Capture DSLR3.2.2 The Card „Settings“Shooting Mode For display of capture mode (set at the camera). Recommended mode is„M“ (manual).- M Exposure time and lens aperture can be set in lines „Av“ and „Tv“. Evenfor the use of profile parameters the mode should be „M“.- P The camera sets the capture parameters exposure time Tv and lensaperture Av automatically.When the photo is taken the automatically used parameters are displayedon card “Shot Conditions”.- Tv The camera automatically chooses the optimal lens aperture Av inrelation to the manually set exposure time. After the picture is taken theautomatically used aperture is displayed in the card Shot Conditions.- Av The camera automatically chooses the optimal exposure time Tv inrelation to the manually set lens aperture. After the picture is taken theautomatically used exposure time is displayed in the card Shot Conditions.Lens aperture,AvExposure time,TvResolutionFor setting the lens aperture. A small aperture number stands for a wideopen lens, a high aperture number for a more closed lens. The depth offocus increases with rising aperture number (= smaller lens aperture). Agarosegels, especially thicker gels, should be photographed with high aperturenumber (= small aperture). Otherwise photos may not be focussed.The largest aperture (= small number) available depends on the zoom factorset. With zoom 55 mm the largest aperture is 5.65, with zoom 35 aperture4 and with zoom 18 the largest possible aperture to be set is 3.5.For setting the exposure time. The time is to be set in dependence ofsample/illumination and lens aperture. For smaller apertures (= high aperturenumber, e.g. 8) exposure times of up to 8 seconds can be necessaryfor a photo of fluorescent gels.For choice of image resolution in pixels. The higher the resolution thebigger the file size.High resolutions will cause longer data transfer times from camera to PCon computers with slow processors and memory below 1 GB RAM. For anefficient operating it is recommended to use a computer with at least 2 GBRAM and a 2.8 GHz processor.BDAdigital Manual, Vers. 02_12


Large + FineMedium + FineSmall + FineSmall S2ISOExposureCompensationEOS 1100DResolution (pixels)Approx. 12.2 MPApprox. 6.3 MPApprox. 3.4 MPApprox. 2.5 MPCompressionFineFineFineFine21Image Capture DSLRFor setting of the sensitivity.In most cases it is advised to use ISO 100. It provides sufficient sensitivityby lowest background noise. Only for the acquisition of very faint signals athigh zoom factors it can be necessary to raise the sensitivity to higher ISOscores.For setting an exposure correction. A fine-tuning of the optimal exposurecan be done in small steps. This function is not available in shooting mode„M“ because lens aperture and exposure time are specifically set in themanual mode.3.2.3 Camera Settings for Typical GelsThe software provides camera settings for two typical gel types in Profiles. Starting withthese settings it is very easy and fast to optimize the camera settings for individual gels.Gel typeEtBr Stained Agarose Gelon UV tableProfile „DNA/EtBr“Shooting Mode M MLens aperture Av 5.6 5.6Exposure time Tv 8 s 1/50 sISO 100 100Coloured PolyacrylamideGelon UV table with yellowconverter plate, without UVfilter on camera lens,e.g. silver or CoomassieBlue stained polyacrylamidegelProfile „Converter“Resolution Medium + Fine Medium + FineBDAdigital Manual, Vers. 02_12


22Image Capture DSLR3.2.4 Further Functions for Image CaptureLive viewon/offFocus bar andAutofocusFor turning on/off the live preview in window „Live Preview“.Due to the high iteration frequency of the picture and forthis reason short exposure times it is possible that the livepreview will not be as bright and focussed as the real gelpicture.Note: For camera protection reasons the live preview isturned off after some minutes without any operation. It canbe turned on again with the button “Live View on”.Button Autofocus triggers the autofocus. As long as the selection box“AF” beside button “Take Picture” is selected it is not necessary to releaseAutofocus additionally before taking the image.MagnificationbuttonThe arrow buttons are for manual focussing. For an easy optical controlthe magnification buttons beside the Live Preview can be used, seebelow.For easy control of image sharpness during manual focussing(see above) an area of the preview image can beenlarged by factor 5. Fit resets the magnification.The desired section for magnification can be choosen withthe red frame. Click on the preview places the magnificationframe at this place.BDAdigital Manual, Vers. 02_12


23Image Capture DSLR3.2.5 Take photo and display settingsTake pictureAFRotate 180°InvertShow GridBlack & WhiteModeSaturationAnalysisExitThis button triggers taking the image. The picture is transferred from thecamera to the computer and it is displayed on card “Image”.The select box „AF“ is selected as default. As long as it is activated thecamera will be automatically focussing before taking the picture.For rotating the picture 180°, for example when the gel is positioned theopposite way round on the illumination table or when the camera is fixedon the darkhood or stand with the camera control panel ahead.For inverting of the gel picture. The use of this function is only sensefulwith black&white pictures.A grid can be displayed on top of the photo. This can be used as controlwhether the gel is positioned in straight form. This is important for an accuratedetection of lanes in a subsequent gel analysis.Activation of this function results in a change of the colour picture to agrey-scale picture.Activation of this function sets areas of the photo to blue or red colour ifthe signal reaches saturation. The photo display automatically switches tothe black&white mode.The pixels of the area to be quantitatively analyzed later must not besaturated, neither true white or true black. That means that the area ofinterest must not be in blue or red colour. This can be achieved by shorterexposure times or with smaller lens apertures (= larger lens aperture number).When using longer exposure times it is possible that the live preview isdarker than the photo. This will cause differences in the saturation displayof preview and photo.For saving the picture in the Biometra-specific BD1 format, JPG or TIFformat and the following transfer to the BDA analysis software. Aftersaving the gel picture will automatically be opened as black&white picturein the analysis partFor closing of the capture window.for further gel analysis.BDAdigital Manual, Vers. 02_12


24Image Capture DSLR3.2.6 Troubleshooting for problems with autofocusRelease of a photo with „Take picture“ automatically triggers the autofocus. In case that thecamera doesn´t succeed with autofocus the message “Out of focus” is displayed.Possible reasons are:- No clear structure on the gel- Sample signal too dark- Sample signal too bright (the UV ruler canoutshine!)- Sample surface is reflecting(Is the gel covered by a foil?Is the white light from aboved yet turned on?)Solutions:With Autofocus:- Set a smaller lens aperture (= larger Av value → better depth of focus)and longer acquisition time Tv- Change the image section: Decrease the zoom (at the camera lens ring)- Turn on white light from above,„Autofocus“ button, turn off white light,disable „AF“, „Take Picture“- Apply a ruler on top of the gel,„Autofocus“ button, remove the ruler,disable „AF“, „Take Picture“- When the UV ruler is too bright: Decrease the acquisition time TvManual (should always lead to a focussed image):Focus manually with the arrow buttons with the help of the 5x magnification area in the imagepreview.BDAdigital Manual, Vers. 02_12


25Image Capture DSLR3.2.7 Basic functionsLoad imageSave imagePrint imageImages saved in JPG, TIF or Biometra specific BD1 format can beloaded to the capture window.The displayed gel picture is saved in JPG, TIF or Biometra specific BD1format by typing in a name. Default is BD1 format which generates ablack&white image including image acquisition camera settings. BD1is standard format in the gel analysis part of the BioDocAnalyze software.A print preview window is opened. It is possible to select the desiredprinter (DIN A4 printer or thermal printer). Then the displayed gel picturecan be printed.Print parameter It can be chosen whether the gel picture is printed with or without camerasettings.3.2.8 The Gel Picture WindowImageShotConditionsCommentsDisplay of the photo or loaded gel picture.Setting parameters of the gel photo or the loaded gel file are shown.File comments can be entered. These comments are only saved in BD1-format files!The comments are printed below the gel photo and can also be seen in theBioDocAnalyze analysis window as “General Comment”.Please regard: It is only possible to print around 20 chars per line and 5lines.BDAdigital Manual, Vers. 02_12


26Image Capture Compact Camera4 BDAdigital Image Capturewith Digital Compact Camera,e.g. PowerShot G10The BDAdigital image capture software is started with a LEFT MOUSE BUT-TON CLICK on the icon „digital camera“.! When starting the BDAdigital capture softwarefor the first time after installation you will beasked for a 4-digit software code to activatethe capture screen.The code comes along with the dongle.The window „Capture digital camera“ is opened and a loading bar indicates that the softwarejust initializes the digital camera.Fig. 4-1Window „Capture digital camera“The line „Camera“ should show e.g. „PowerShot AG10“. In case that only „Model“ is shownthe camera is not correctly installed or not switched on. The camera needs to be on replayand then shows „PC“ on the camera display (display is not existing at all camera models).When the capture window is opened it starts with the camera settings of the last opened profile.BDAdigital Manual, Vers. 02_12


27Image Capture Compact Camera4.1 The Image CaptureThese are the typical steps for image capture:10. Switch on the live preview: .11. Place the electrophoresis gel on the transilluminator.12. Switch on the light source of the darkhood.13. Place the gel with the help of the live preview in the transilluminator center.14. Choose the desired zoom area by window„Settings“:15. Choose the appropriate settings profile:16. Take a photo:17. If necessary optimize the exposure time Tv and the lens aperture Av in window „Settings“in set „Shooting Mode“ „Manual“ and take anotherphoto.18. Save and print the image:Please see details of the different functions in section 4.2.BDAdigital Manual, Vers. 02_12


28Image Capture Compact Camera4.2 Functions and Capture ParametersThe window „Capture digital camera“ is widely self-explaining and very similar to generalknown parameters in photography. In spite of that the individual functions are explained inthe following.4.2.1 Profiles with Capture ParametersProfileSaveClearThis includes some profiles with working parameters for the image acquisition ofcertain gel types.A mouse click on the profile will set the parameters in the camera. The correspondingparameters are shown in the cards Settings and Advanced. It is essential thatthe Shooting Mode is „manual“ otherwise the settings shown in the card Settingswill not really be the used parameters.It is also possible to enter names for individual settings. After typing in the newname and setting the parameters the new profile has to be saved .Switch off of the „live image“ will accelerate the change of profiles.This saves user-defined profiles under the active profile name.Before saving you should check whether already a profile with the same name existsbecause it would be overwritten.This deletes the active profile. The Biometra saved profiles can not be deleted.4.2.2 The Card „Settings“Shooting Mode For choice of capture mode. Typical settings are „Manual“ or „Auto“.- Manual Exposure time and lens aperture can be set in lines „Av“ and „Tv“. Evenfor the use of profile parameters the mode should be „Manual“.It should be kept in mind that the camera can not set the largest apertures(= small aperture number) together with a large zoom factor. In thesecases the camera automatically chooses the largest possible lens aperture.After the picture is taken the aperture display on the card is actualizedto the really used one.- Auto The camera sets the capture parameters exposure time and lens apertureautomatically. Be aware that these settings are not displayed in thecamera settings.BDAdigital Manual, Vers. 02_12


29Image Capture Compact CameraBe aware that the displayed and printed settings are not the true settingsthe cameras has automatically chosen for the photo!- Tv The camera automatically chooses the optimal lens aperture in relationto the manually set exposure time. After the picture is taken the automaticallyused aperture is displayed in the card Settings.- Av The camera automatically chooses the optimal exposure time in relationto the manually set lens aperture. After the picture is taken the automaticallyused exposure time is displayed in the card Settings.Lens aperture,AvExposure time,TvResolutionFor setting the lens aperture. A small aperture number stands for a wideopen lens, a high aperture number for a more closed lens. The depth offocus increases with rising aperture number (= smaller lens aperture). Agarosegels, especially thicker gels, should be photographed with high aperturenumber (= small aperture). Otherwise photos may not be focussed.For setting the exposure time. The time is to be set in dependence ofsample/illumination and lens aperture. For smaller apertures (= high aperturenumber, e.g. 8) exposure times of up to 8 seconds can be necessaryfor a photo of fluorescent gels.For choice of image resolution in pixels. The higher the resolution thebigger the file size.High resolutions will cause longer data transfer times from camera to PCon computers with slow processors and memory below 512 MB RAM. Foran efficient operating it is recommended to use a computer with at least 1GB RAM and a 2.8 GHz processor.In pixels PowerShot G10 PowerShot G9 PowerShotA640PowerShotA620/G6HighMedium1Medium2LowZoom4416 x 33123456 x 25922592 x 19441600 x 12004000 x 30003264 x 24482592 x 1994640 x 4803648 x 27362816 x 21122272 x 1704640 x 4803072 x 23042592 x 19442048 x 1536640 x 480The optical zoom can be set with the slider or by typing in a value between0 and 13 (G10, G9), 0 and 8 (A640/A620), 0 and 12 (G6/G5/G3) resp. 1 to10 (G2).A higher zoom reduces the amount of light that reaches the camera sensors.This can cause difficulties for the autofocus. When the autofocusdoes not succeed to take a focussed picture although there is a clear objectin the image center please- set a longer exposure time (Shooting Mode Manual)- set less zoom.- Use the function “AF Lock” for fixation of the autofocus. (see 3.2.5)- use the function „manual Focus“ (MF button on camera back). Thismanual focus is not available for use with remote control by the computer.For use of the manual focus please disconnect the USB cableof the camera from the PC and run the camera separately. Please setalso the macro mode (flower symbol on camera back). The photos aresaved on the compact flash card.BDAdigital Manual, Vers. 02_12


30Image Capture Compact Camera4.2.3 The Card „Advanced“QualityISOFlashExposureCompensationWhite BalanceAutofocusDistanceFor choice of compression of picture data in JPG format. In generalquality „normal“ will be sufficient. Quality „superfine“ with only low compressionneeds more saving capacity and time for image analysis.For setting of the sensitivity. Value ISO 400 is recommended for low illuminationand big zoom, but in contrast to photos at ISO 50 a certain backgroundnoise appears.In most cases it is advised to use ISO 50. Only for the acquisition of veryfaint signals at high zoom factors it can be necessary to raise the sensitivityto ISO 400.For activation or deactivation of the flash. Applications with darkhoodsshould be done with flash „off“. Flash „on“ or „auto“ can be used for photographswith stand in a dark room, but reflections on the gel surface can notbe excluded.For setting an exposure correction. A fine-tuning of the optimal exposurecan be done in small steps.This function is not available in shooting mode „Manual“ because lens apertureand exposure time are specifically set in the manual mode.For setting the white balance. Colors can be mirrored more true to originalwhen the illumination source is set. This factor is of only minor relevancefor black&white photos.For definition of distance where the autofocus will look for the sample.For image acquisition with Biometra darkhoods „Close up“ has to be set.This setting will lead within the limited distance of camera to gel to wellfocussedpictures over the whole range of zoom.BDAdigital Manual, Vers. 02_12


31Image Capture Compact Camera4.2.4 Camera Settings for Typical GelsThe software provides camera settings for two typical gel types in Profiles. Starting withthese settings it is very easy and fast to optimize the camera settings for individual gels.Gel typeEtBr Stained Agarose Gelon UV tableProfile „DNA/EtBr“Shooting Mode Manual ManualLens aperture Av 6.3 4.0Exposure time Tv 4 s 1/125 sAutofocus distance Close up Close upISO 50 50Flash Off OffQuality Normal NormalColoured PolyacrylamideGelon UV table with yellowconverter plate, without UVfilter on camera lens,e. g. silver or CoomassieBlue stained PolyacrylamidegelProfile „Converter“Resolution Medium 1 Medium 1Zoom e. g. 5 e. g. 5compen-Exposuresation0 0White balance Auto FluorescentBDAdigital Manual, Vers. 02_12


32Image Capture Compact Camera4.2.5 Further Functions for Image CaptureAF LockFunction for fixation of the autofocus. This function can beused for photos which cannot be focussed with the autofocus.This may happen with gels which have no bands orhave only very weak bands in the gel center or when usinga high zoom.The principle of this function is that first a clear bright tool isplaced in the center and the autofocus is directed to that.After fixing the autofocus in this position the tool is removedand the photo can be taken.Please note:When you are changing the zoom you have to set the autofocusagain!Procedure:A. with fluorescent agarose gels:a) Switch on white light from above (+ place a thin ruler onthe gel),activate the autofocus button (or take a photo),activate the AF Lock function,switch off the white light from above (and remove theruler),switch on the UV light,take the photo.b) place a fluorescent ruler on the gel,activate the autofocus button (or take a photo),activate the AF Lock function,remove the ruler,take the photo.B. with coloured gels on converter plate:Place a non-fluorescent ruler on the gel,activate the autofocus button (or take a photo),remove the ruler,take the photo.DelayWith activated Delay function the camera updates the internalsettings with a 5 seconds delay after the lastchange of settings parameters in the cards Setting andAdvanced. The use of the delay function is recommendedfor a faster operating if the user wants to change severalparameters before taking the next picture.If it is intended only to change one parameter it is morepractical to deactivate the delay function. Then the camerawill react directly after the parameter on the card ischanged.BDAdigital Manual, Vers. 02_12


RefreshLive imageon/offAutofocus33Image Capture Compact CameraIt is possible to manually trigger the updating of internalcamera settings with the Refresh button. Then it is not necessaryto wait the 5 seconds standard delay for automaticupdating.For switch on/off the live preview in window „Live Preview“.Due to the high iteration frequency of the picture andfor this reason short exposure times it is possible that thelive preview will not be as bright and focussed as the realgel picture.For manual activation of the autofocus. This can behelpful in case that the camera fails to focus automatically.4.2.6 Take photo and display settingsTake pictureRotate 180°InvertBlack&WhiteModeSaturationClick on the button releases the camera. The picture is transferred fromcamera to PC and is displayed in the gel window in the right of the Capturewindow.The “additional” functions Rotate, Invert, Black&White Mode and Saturationare deactivated after taking a photo or printing. These functions haveto be activated again when it is desired to have.For rotating the picture 180°, for example when the gel is positioned theopposite way round on the illumination table or when the camera is fixedon the darkhood or stand with the camera control panel ahead.For inverting of the gel picture. The use of this function is only sensefulwith black&white pictures.Activation of this function results in a change of the colour picture to agrey-scale picture.Activation of this function sets areas of the photo to blue colour if the signalreaches saturation. The photo display automatically switches toblack&white mode.The pixels of the area to be quantitatively analyzed later must not besaturated, neither true white or true black. That means that the area ofinterest must not be in blue colour. This can be achieved by shorter exposuretimes or with smaller lens apertures (= larger lens aperture number).When using longer exposure times it is possible that the live preview isdarker than the photo. This will cause differences in the saturation displayof preview and photo.BDAdigital Manual, Vers. 02_12


34Image Capture Compact CameraAnalysisExitFor saving of the picture in the Biometra-specific BD1 format, JPG or TIFformat and the following transfer to the BDA analysis software. Aftersaving the gel picture will automatically be opened as black&white picturein the analysis part for further gel analysis.For closing of the capture window.4.2.7 Basic functionsLoad imageSave imagePrint imageVia the folder icon already saved pictures in JPG, TIF or Biometra specificBD1 format can be loaded to the capture window.Via disc icon the active gel picture is saved in JPG, TIF or Biometra specificBD1 format by typing in a name. Default is BD1 format which generatesa black&white image including image acquisition camera settings.BD1 is standard format in the gel analysis part of the BioDocAnalyzesoftware.A print preview window is opened. It is possible to select the desiredprinter (DIN A4 printer or thermal printer). Then the displayed gel picturecan be printed.4.2.8 The Gel Picture WindowImageShot ConditionsCommentsDisplay of the photo or loaded gel picture.Setting parameters of the gel photo or the loaded gel file are shown.The complete parameters are only saved with photos in BD1 files.File comments can be entered. These comments are only saved in BD1-format files!The comments are printed below the gel photo and can also be seen in theBioDocAnalyze analysis window as “General Comment”.Please regard: It is only possible to print around 20 chars per line and 5lines.BDAdigital Manual, Vers. 02_12


35Service5 ServiceIn case you have any problem with the device please contact our service division or yourlocal Biometra dealer.Biometra GmbHService DepartmentRudolf-Wissell-Straße 14-16, D-37079 Göttingen, GermanyTel: +49 551 50686-10 or -12Fax: +49 551 50881-11e-mail: service@biometra.comPlease follow the return instructions when returning the device:Return instructionsPlease contact our service department for providing a return authorization number (RAN).This number has to be applied clearly visible to the outer box.Returns without the RAN will be not be accepted!Return only faulty devices. For any technical problem that is not clearly identifiable as adevice failure, please contact the Service Department of Biometra.Use the original packing or a similar robust packing when returning the material.The darkhood must be shipped on a pallet. The transilluminator has to removedfrom the hood and must be shipped separately! The drawer must be secured withsome packing material to avoid that the drawer is moving and touching the UVprotection shield during transport.Mark the outer packing with “CAUTION! SENSITIVE ELECTRONIC INSTRUMENT!”Please include a precise description of the problem and preferably one that also describesby which procedure the failure occurs or how it is caused.Important:Clean every part of the device from residues such as chemical, radioactive anddangerous biological contamination. Please confirm in writing (EquipmentDecontamination Certificate) before every return that the device is free of radioactiveand dangerous biological contamination. Contaminated devices sent to Biometra willbe refused!The sender will be liable for the repair order in case of damage resulting from aninadequate decontamination of the device.Please include a note with the following information:a) Sender’s name and addressb) Contact person and phone number in case of inquiry.BDAdigital Manual, Vers. 02_12


36Service6 Equipment Decontamination CertificateTo enable us to comply with german law (i.e. §71 StrlSchV, §17 GefStoffV and §19 ChemG)and to avoid exposure to hazardous materials during handling or repair, please complete thisform, prior to the equipment leaving your laboratory.COMPANY / INSTITUTE ____________________________________________________________________ADDRESS ________________________________________________________________________________PHONE NO _______________________________ FAX NO _______________________________________E-MAIL ___________________________________________________________________________________EQUIPMENT Model Serial No________________________________________________________________________________________________________________________________________________If on loan / evaluation Start Date: ________________ Finish Date ____________________Hazardous materials used with this equipment___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________Has the equipment been cleaned and decontaminated? YES / NO (delete)Method of cleaning / decontamination___________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________NAME ________________________________(HEAD OF DIV./ DEP./ INSTITUTE / COMPANY)SIGNED ______________________________POSITION ___________________________DATE _______________________________PLEASE RETURN THIS FORM TO BIOMETRA GMBH OR YOUR LOCAL BIOMETRA DISTRIBU-TOR TOGETHER WITH THE EQUIPMENT.PLEASE ATTACH THIS CERTIFICATE OUTSIDE THE PACKAGING. INSTRUMENTS WITHOUTTHIS CERTIFICATE ATTACHED WILL BE RETURNED TO SENDER.BDAdigital Manual, Vers. 02_12


37ServiceGeneral Information for Decontamination:Please contact your responsible health & safety officer for details.Use of radioactive substances:Please contact your responsible person for details.Use of genetically change organism or parts of those:Please contact your responsible person for details.BDAdigital Manual, Vers. 02_12


38Service7 DisposalDue to the application in a laboratory the system must be decontaminated before return aselectronic waste.Hinweisfür die Entsorgung von ElektroaltgerätenNoteRenseignementfor disposal of electric / electronicalwastedu traitement des déchets desappareils électrique / électroniqueDas Symbol der durchgestrichenen Abfalltonne bedeutet für unsere Kunden in Deutschland,daß dieses Produkt von der Firma Biometra kostenlos zur Entsorgung zurückgenommenwird.Zu diesem Zweck kontaktieren Sie bitte unsere Service-Abteilung!Außerhalb Deutschlands wenden Sie sich bitte an den für Sie zuständigen Händler.Dieses Symbol gilt nur in Staaten des EWR*.*EWR = Europäischer Wirtschaftsraum, umfasst die EU-Mitgliedsstaaten sowie Norwegen,Island und Liechtenstein.----------------------------------------------------------------------------------------------------------------------------------------------------------------------This symbol (the crossed-out wheelie bin) means, that this product should be brought to thereturn or separate systems available to end-users according to yours country regulations,when this product has reached the end of its lifetime.For details, please contact your local distributor!This symbol applies only to the countries within the EEA*.*EEA = European Economics Area, comprising all EU-members plus Norway, Iceland andLiechtenstein.----------------------------------------------------------------------------------------------------------------------------------------------------------------------Cet symbole (conteneur à déchets barré d´une croix) signifie que le produit, en fin de vie,doit être retourné à un des systèmes de collecte mis à la disposition des utilisateurs finauxen conséquence des régulations par la loi de votre pays.Pour des information additionel nous Vous demandons de contacter votre distributeur!Cet symbole s´applique uniquement aux pays de l´EEE*.*EEE = Espace économique européen, qui regroupe les États membres de l´UE et la Norvège,Islande et le Liechtenstein.BDAdigital Manual, Vers. 02_12

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