Bio-rad EXQuest Spot Cutter Manuel d'utilisateur

ixPreface1. About This DocumentThis user guide is designed to be used as a reference in your everyday use of PDQuest™. It provides detailed informatio

Viewing and Editing Images3-21Fig. 3-14. Transform command.The preview window in the Transform dialog shows a smaller view of the selected image. Cha

PDQuest User Guide3-22Fig. 3-15. Transform dialog box.You can use regular viewing tools like Zoom Box and View Entire Image in the preview window to

Viewing and Editing Images3-23Note: If you are using the Transform window in conjunction with the Multi-channel Viewer, you can adjust the display of

PDQuest User Guide3-24Fig. 3-16. Two views of the Frequency Distribution histogram.Gamma SliderSome images may be more effectively visualized if thei

Viewing and Editing Images3-25ResetIf at any time you want to return to an unmodified view of the scan data, click Reset.Applying the SettingsClick OK

PDQuest User Guide3-26Invert DisplayThe Invert Display checkbox flips light bands on a dark background to dark bands on a light background, and visa v

Viewing and Editing Images3-27Select Crop from the Image menu or toolbar, and drag the cursor on the image, creating a box. Everything outside the cro

PDQuest User Guide3-28Fig. 3-18. Crop box and pop-up Crop dialog.If you select Crop, your cropped image will be displayed in the image window. If you

Viewing and Editing Images3-29image detail. The crosshair will make it easier to position the box in the other images so that it encloses the same are

PDQuest User Guide3-30Fig. 3-19. Flipping and rotating commands.Note: These actions will erase any analysis you have performed on an image. You will

PDQuest User Guidex2. Overview of Raw 2-D Gel ElectrophoresisRaw 2-D electrophoresis is a method for separating proteins and nucleic acids in a sample

Viewing and Editing Images3-31Select Custom Rotation from the Image > Rotate menu or Image toolbar. A green “plus” sign will appear next to your cu

PDQuest User Guide3-32Note: If you want to center your arrow on a particular point on the image (e.g., to align along a particular lane), you can use

Viewing and Editing Images3-33Fig. 3-21. Filtering commands.Note: Since filtering is an irreversible process, you will be asked if you want to create

PDQuest User Guide3-34To open the Wizard, select Image > Filter Wizard or click the Filter Wizard button on the Image Tools toolbar.Fig. 3-22. Fil

Viewing and Editing Images3-35noise peaks at the high end of the range (right end of the plot). This type of noise is common in electronic cameras wit

PDQuest User Guide3-36Step 3: Begin FilteringAfter you have completed your selections, the filter name and size will be displayed at the bottom of the

Viewing and Editing Images3-37• MidValue. This filter is useful for suppressing uniform noise within an image; however, it worsens the effect of peppe

PDQuest User Guide3-38If you choose to copy and filter, you will be asked to enter a new name and/or version number for the new copy before the operat

Viewing and Editing Images3-39Creating a Text OverlayTo create a text overlay, click the Text Tool, then click on the image at the spot where you want

PDQuest User Guide3-40Line ToolYou can use the Line Tool on the Text Overlay toolbar to draw a line between text and an image feature, or between any

Prefacexiexpression; and companies and institutions can cross-identify and catalog hundreds of thousands of protein species at the cellular level. Thi

Viewing and Editing Images3-41Note: If you are pasting into an image with a different pixel size (i.e., resolution), you will receive a message that t

PDQuest User Guide3-42

4-14. Detecting and Editing SpotsThis chapter describes how to detect and edit spots using PDQuest.4.1 Selecting Spot Detection ParametersThe Spot Det

PDQuest User Guide4-2Fig. 4-1. Spot Detection Parameter Wizard.The Wizard will open, and the name of the scan will be displayed below the preview wind

Detecting and Editing Spots4-3Fig. 4-2. Selecting a new image in the Spot Detection Wizard.The control panel in the Wizard is designed to guide you th

PDQuest User Guide4-4Fig. 4-3. Image with large, small, and faint spots defined.4.1.b Step 2. Test SettingsIn this step, you first see how many spots

Detecting and Editing Spots4-5Fig. 4-4. Spot crosshairs marked in the Spot Detection Wizard.If all the spots you want to identify have been detected,

PDQuest User Guide4-6Min PeakIf increasing the Sensitivity setting or selecting a new Faint Spot still fails to find some faint spots, you can lower t

Detecting and Editing Spots4-7StreaksProtein gels frequently display streaking in areas of high spot concentration. Click the Streaks tab to access th

PDQuest User Guide4-8Note: You should first attempt to find spot centers using these default settings before attempting to adjust them.If you know the

PDQuest User GuidexiiSample ExperimentsValuable information can be learned by exposing cells to a set of specific experimental conditions and subseque

Detecting and Editing Spots4-9Click OK. The parameter set will now be available for processing all similarly detected gel scans.To load previously sav

PDQuest User Guide4-10Fig. 4-5. Automated Detection and MatchingAutomated Detection dialogThe Automated Detection and Matching tool combines several p

Detecting and Editing Spots4-11As indicated on the dialog, you can set the order of the members by dragging them in the list. This order will be used

PDQuest User Guide4-124.3 Filtered and Gaussian ImagesWhen spots are detected in PDQuest, the original gel scan is filtered and smoothed to clarify th

Detecting and Editing Spots4-13Fig. 4-7. Example of a Scanset.Note: Use the Assign tool and Configure Subwindows command on the main toolbar to arrang

PDQuest User Guide4-144.4 Spot Crosshairs and EllipsesSpot crosshairs mark the centers of spots in the Gaussian image, while spot ellipses show their

Detecting and Editing Spots4-15Note: Spots without crosshairs in the Filtered and Raw 2-D Scan images have not been detected and are not included in t

PDQuest User Guide4-16Note: You can add and remove spots in the MatchSet and/or the scanset. Note that, after a MatchSet has been created, subsequent

Detecting and Editing Spots4-17Fig. 4-10. Adding a spot.Note: Use Plot Cross-section (Ctrl+t, View > View Density submenu) to aid in accurately pos

PDQuest User Guide4-18Note: It is also possible to add spots on Raw 2-D scans when the Filtered and the Gaussian images are loaded.Fig. 4-11. Removin

1-11. Introduction1.1 Overview of PDQuestPDQuest is a software package for imaging, analyzing, and databasing Raw 2-D electrophoresis gels.The softwar

Detecting and Editing Spots4-19Spots defined using the boundary tools are not Gaussian modeled, even though they appear in the Gaussian image. However

PDQuest User Guide4-20Fig. 4-13. Creating a spot contour.To edit the boundary, position your cursor on the border with the contour tool. Your cursor w

Detecting and Editing Spots4-21Fig. 4-14. Creating a freehand boundary.To edit the boundary, position your cursor on the border and drag across the li

PDQuest User Guide4-22To reposition a spot boundary, make sure the Contour, Freehand, or Select tool is active, then position your cursor in the middl

Detecting and Editing Spots4-23To restore all unmatched cancelled spots in a MatchSet, select Restore Unmatched Spots from the Match > Edit Matches

PDQuest User Guide4-24You can also use the Highlight Saturated Pixels in the Transform window to identify regions of saturation in the image.Faint Spo

Detecting and Editing Spots4-25Note: This formula results in more accurate quantitation of imaged spots than summing the intensities of the pixels in

PDQuest User Guide4-26To cancel all low quantity spots in the set, select Spots > Low Quantity Spots > Cancel Low Quan. Spots and click in the M

Detecting and Editing Spots4-27• Gaussian fit. PDQuest determines how well the spot fits the Gaussian model and assigns a value based on this fit.• X

PDQuest User Guide4-28To cancel all low quality spots in the set, select Spots > Low Quality Spots > Cancel Low Qual. Spots and click in the Mat

PDQuest User Guide1-2Mass Spec AnalysisPDQuest is part of Bio-Rad’s ProteomeWorks protein analysis package, and controls Bio-Rad’s ProteomeWorks Spot

Detecting and Editing Spots4-29Click OK to complete the search. The spot will appear highlighted and numbered on the image.

PDQuest User Guide4-30

5-15. MatchSetsAfter the protein spots in your gels have been detected, you are ready to compare spots across gels. To do so, you must create a MatchS

PDQuest User Guide5-2A MatchSet can consist of one gel or many gels, depending on the type and size of the experiment. The MatchSet is displayed in a

Matchsets5-3spot quantities measured in O.D.s cannot be compared to spot quantities measured in counts). Qualitative comparisons are still valid.5.1 C

PDQuest User Guide5-45.1.a Create a MatchSetFig. 5-3. Create MatchSet dialog.At the top of the Create MatchSet dialog, enter a name for the MatchSet i

Matchsets5-5If you are creating a level 1 MatchSet, use the Add button to select the Gaussian images to be included in the MatchSet. The names of the

PDQuest User Guide5-6Raw 2-D and Filtered images are in included in the MatchSet by default. Including the Filtered images allows you to compare the G

Matchsets5-7member images will not affect other MatchSets. This option uses more space on and requires you to manage disk utilization more carefully.T

PDQuest User Guide5-8Fig. 5-6. Automated Detection and Matching dialog.When you have completed Step 1 Select Gels to Analyze and Step 2 Detect spots,

Introduction1-3Fig. 1-1. Representation of the pixels in two digitally imaged spots in a gel.For a data object to be visible and quantifiable, the int

Matchsets5-9If you only want to perform gel selection and spot detection and do not want to create a MatchSet at this time, check the Disable this ste

PDQuest User Guide5-10With your Master created, you are ready to begin matching and editing spots in the MatchSet (see the following chapter).Displayi

Matchsets5-11Fig. 5-7. Match Menu and toolbar.Using landmarks, PDQuest automatically matches most of the spots in the MatchSet. You then review the re

PDQuest User Guide5-12Each matched spot is marked with a green letter in the Master and the matched gels. Unmatched spots in the member gels are marke

Matchsets5-13Fig. 5-9. Edit MatchSet dialog.Note: Any annotations, analysis sets, etc. in the MatchSet will be lost if you replace the Master template

PDQuest User Guide5-14Removing MatchSet MembersTo remove a MatchSet member, select the gel to be removed from the member list and click the Remove but

Matchsets5-15Fig. 5-10. Selecting a spot to landmark.Select Landmark from the Match menu, Match toolbar, or right-click menu, and click on the spot in

PDQuest User Guide5-16Fig. 5-11. Landmarking a spot.If the program is unsure about positioning the landmark, the area in which the spot was expected w

Matchsets5-17The number of landmarks required will vary depending on the number and quality of the gels in the MatchSet. Gels with well-resolved spots

PDQuest User Guide5-18algorithm PDQuest has used in previous versions. If you select this method, the primary phase can be thought of as "auto-l

PDQuest User Guide1-41.3 PDQuest Workflow Fig. 1-2. Steps involved in using PDQuest. Image Acquisition PDQuest can acquire images of gels using Bio-Ra

Matchsets5-19Note: Most MatchSet gels require at least two landmarks before auto-matching will occur. The gel that was used as the template for the Ma

PDQuest User Guide5-20Primary MatchingFig. 5-12. Automated Matching - Primary and Extended options.Use the Primary Matching tab to find landmarks auto

Matchsets5-21Set the matching precision slider towards strict or liberal, depending on the degree of precision you prefer. The most rigid setting you

PDQuest User Guide5-22Mark Landmarks command (F8) on the Match menu and toolbar.• Spots added to the Master are labeled with blue boxes. These are als

Matchsets5-23Fig. 5-13. Vector offsets indicate that these two spots have been mismatched.5.6 CybergelsPDQuest needs to know the pH gradient of a gel

PDQuest User Guide5-24Fig. 5-14. Overlapping gels with narrow pH rangeTo combine gels with narrow-range pHs, select the most acidic gel as your Master

Matchsets5-25Fig. 5-15. Combine Narrow-range gels.Use the Add From Member dropdown list to add successive gels to the Master. Add additional gels in o

PDQuest User Guide5-26Landmarking Gels with Different pH GradientsIf you are combining gels with different pH gradients into the same Master, you will

Matchsets5-27Fig. 5-16. Auto-add Spots to Master dialog.In the dialog box, select the MatchSet member from the Select Member popup box. The MatchSet w

PDQuest User Guide5-28threshold value directly into the box to the left of the slider. As you adjust the threshold, spots that no longer meet that thr

Introduction1-5Spot Identification Now you are ready to identify the spots in the gel. The Spot Detection Wizard automates the process of selecting th

Matchsets5-29Select Add Spot to Master from the Match menu or toolbar, and click on the center of the unmatched spot in the member. The cursor will ju

PDQuest User Guide5-30Fig. 5-17. Edit matches submenu commands.Manual MatchingAfter you have landmarked numerous spots and reviewed the results of aut

Matchsets5-31Otherwise, if auto-matching has missed a spot that should have been matched, you can landmark it to improve the alignment and modeling of

PDQuest User Guide5-32Graph Partial Matches displays histograms of each partially matched spot in the Master. Select the command from the submenu and

Matchsets5-33Fig. 5-19. Graph Erratic Responses; each bar represents the spot’s quantity in a gel.Note: Histograms can only be displayed for one regio

PDQuest User Guide5-34Manual matches and landmarks will not be removed. Because this command is irreversible, you will be prompted to complete the ope

Matchsets5-35Fig. 5-20. Example of a higher level MatchSet.Creating a Higher level MatchSetUse the Create Matchset dialog, Match > New MatchSet to

PDQuest User Guide5-36users, you should move the lower-level MatchSets to a shared file server and create it there.Note: If a higher level MatchSet an

Matchsets5-37Click Add to open the Select Member dialog where you can highlight the MatchSets you want to include. Click open and they will display in

PDQuest User Guide5-38Fig. 5-22. Matching Summary dialogMember information lists each gel in the MatchSet and information regarding each gel including

PDQuest User Guide1-6Matching and Editing After you have detected the spots in a gel or set of gels, you are ready to create a matchset. A matchset is

Matchsets5-39Replicate Group InformationThe Replicate group information lists the replicate groups with the number of members in the replicate group,

PDQuest User Guide5-40

6-16. Analysis ToolsThe tools on the Analyze menu are designed to help you identify and compare spots of interest in a MatchSet. Analysis sets and ann

PDQuest User Guide6-2Replicate Group quantitation is selected, the bars represent the spot’s quantity in each group. See11.2, Histogram Graphs for a m

Analysis Tools6-3At the top of the review tool window, select All Spots to display histograms of all the spots in the MatchSet or Analysis Set to disp

PDQuest User Guide6-4Fig. 6-3. Reviewing spots using the Review Tool.You can create an arbitrary analysis set (section7.1, Analysis Sets ) out of spot

Analysis Tools6-56.2 Image Stack ToolThe Image Stack Tool allows you to scroll through the images in a scanset or MatchSet layered on top of one anoth

PDQuest User Guide6-6In the stack tool window, all available gels are listed in the Select gels to display field. To select an image to display, click

Analysis Tools6-7Note: Spot flags only affect the images you select for display from the list of members.6.3 Scatter Plot ToolThe Scatter Plot Tool sh

PDQuest User Guide6-8Fig. 6-5. Scatter Plot dialog.The quantity of each spot in the first item (X-axis) is plotted on a log scale against its quantity

P/N 4000129-14 RevAPDQuest™User Guide for Version 7.1Windows and Macintosh

Introduction1-7Publish Results When your analysis is complete, you can print your experimental data or export it to another system for further analysi

Analysis Tools6-9will fall on the black center line in the graph (slope = 1.00). If the quantities are not the same, the point will fall above or belo

PDQuest User Guide6-10Fig. 6-6. Replicate Groups submenu.In the dialog box, enter a name for the replicate group, then click each duplicate gel in the

Analysis Tools6-11Quantitating a Replicate GroupAfter you have created a replicate group, you can calculate the average spot quantities in the members

PDQuest User Guide6-12Fig. 6-9. Quantitation table displaying replicate group quantitation.Click the spot whose quantitation you want to see. If you s

Analysis Tools6-136.5 Group ConsensusThe Group Consensus tool displays a list of all replicate groups associated with the current MatchSet. The purpos

PDQuest User Guide6-14Fig. 6-11. Replicate Group ConsensusAt the top of the Group Consensus tool is the Consensus Summary listing all replicate groups

Analysis Tools6-15column lists the number of spots that appear on one gel and can be matched to more than one spot on one or more of the other gels.Fi

PDQuest User Guide6-16cycle through the spots in the active group. The Review Tool displays a quantity graph of the selected spot. The bars in the gra

Analysis Tools6-176.5.c Global ActionsGlobal actions are much the same as the adding and removing of individual spots but are performed on all the spo

PDQuest User Guide6-18Fig. 6-13. Enter Sample AttributesWith the Enter Sample Attribute window open, click the cell under the Sample heading that corr

PDQuest User Guide1-8SCSI: Required for all Bio-Rad imaging devices except the Gel Doc, ChemiDoc, ChemiDoc XRS, and VersaDoc systems. Adaptec SCSI ca

Analysis Tools6-19If the sample you wish to add is not in the list, click New to create a new sample. This opens the Edit Sample Dialog. Fig. 6-15. Cr

PDQuest User Guide6-20attributes. Select the attribute or attributes you wish to add to the list and click Done. Or, if you wish to create a new attri

Analysis Tools6-21analysis sets based on the attribute values. (See Section 7.1, “Analysis Sets” for information on creating analysis sets.)Fig. 6-17.

PDQuest User Guide6-22Fig. 6-18. Creating Sample PairsTo create a sample pair, highlight a sample inn the left column and a sample in the right and th

Analysis Tools6-23Note: Importing sample pairs will overwrite any pair selections you have already created containing samples that match imported pair

PDQuest User Guide6-24Fig. 6-19. Normalize dialog box for member images.In the dialog box, check the Enable Normalization box to activate normalizatio

Analysis Tools6-25Pipetting error compensation is only available if you have calibrated the gels using Calstrips and entered the number of counts load

PDQuest User Guide6-26Step 2: Click Create then select Arbitrary form the Select Set type dialog. This opens the Arbitrary Analysis Set template.Fig.

Analysis Tools6-27The raw quantity of each spot in a gel will be divided by the total quantity of the spots in the analysis set in that gel, according

PDQuest User Guide6-28This model is useful if you want to correct for known variations in samples across gels (e.g., the amount of cells that went int

Introduction1-91.5 InstallationWindowsNote: Windows NT and 2000 users: You must be a member of the Administrators group to install Discovery Series so

Analysis Tools6-296.8 MrpI DataIn a MatchSet, you can enter the molecular weight and isoelectric point values for your known protein spots. With this

PDQuest User Guide6-30Entering MrpI Values for Known SpotsTo determine MrpI values for all the spots in the MatchSet, you first need to enter the valu

Analysis Tools6-31For a graphical display of the overall trend of MrpI values across the entire gel, first make sure the Master subwindow is active, t

PDQuest User Guide6-32With your higher level MatchSet open, select Transfer MrpIs from the Analyze > MrpI Standards submenu. In the first pop-up bo

Analysis Tools6-33Fig. 6-24. Spot number submenu.With the MatchSet open and active, select Plot SSP Grid (CNTRL +F9) from the submenu to display the S

PDQuest User Guide6-34Display All SSPs displays SSP numbers next to every spot in every open window. Transferring SSP Numbers in a higher level MatchS

Analysis Tools6-353-4=C 8.0-8.5=L 4-5=D 8.5-9.0=M 5.0-5.5=E 9-10=N 5.5-6.0=F 10-11=P 6.0-6.5=G 11-12=Q 6.5-7.0=H 12-14=RDSNs have the format ABnn. “A”

PDQuest User Guide6-36Transferring DSNs in a Higher level MatchSetTransfer DSNs is used to copy the DSNs from one higher level MatchSet member to the

7-17. Analysis Sets and AnnotationsAnalysis sets and annotations are tools to help you organize and analyze your spot data.Analysis sets allow you to

PDQuest User Guide7-2Boolean Analysis Sets: Are created by comparing two or more other analysis sets. For example, set C could be made up of those spo

PDQuest User Guide1-10a folder called The Discovery Series in the Preferences folder in your System Folder; this contains the Help file and various sy

Analysis Sets and Annotations7-3Fig. 7-1. Analysis Set Manager The top portion of the analysis set lists the analysis sets associated with the current

PDQuest User Guide7-4Count - Indicates the number of spots that match the analysis set criteria. Click the column header to organize the list accordin

Analysis Sets and Annotations7-5Fig. 7-2. Select the Analysis Set type you wish to create.In the Select Set Type dialog, select the type you want to c

PDQuest User Guide7-6To delete a saved set, click on the button below the Edit heading in the ASM and select Delete from the list. This permanently re

Analysis Sets and Annotations7-7Fig. 7-3. Qualitative Analysis Set dialog.Enter a name and description of the analysis set.Note: If you have Normaliza

PDQuest User Guide7-8must be detected in >50% of the gels in the group to be included. This is important in qualitative analysis because the analys

Analysis Sets and Annotations7-9Fig. 7-4. Quantitation Analysis Set dialogEnter a name and description of the analysis set.

PDQuest User Guide7-10Note: If you have Normalization enabled, normalization parameters will be used for spot quantities. See Section 6.7, Normalizati

Analysis Sets and Annotations7-11here is you are given a view of which spots will be included or excluded from the analysis set.Do you want to look fo

PDQuest User Guide7-12spots in A.Click on the Save button at the bottom of the dialog box to add the analysis set to the ASM. Be sure to enter a name

Introduction1-11Note: Some parallel port devices such as zip drives may be incompatible with HSKs. Please check with your peripherals vendor.The code

Analysis Sets and Annotations7-13Fig. 7-5. Statistical Analysis TypeStatistical analysis sets only work with replicate groups or classes, because the

PDQuest User Guide7-14Refer to the following table to determine the number of gels per group for you to run a specific test. The Wilcoxon test is only

Analysis Sets and Annotations7-15Step 6: Choose to compare Classes and select the select the classes by clicking on the drop down buttons for A and B.

PDQuest User Guide7-16Fig. 7-6. Arbitrary Analysis setNo SpotsThe No spots option creates an empty analysis set to which you can add any spots you cho

Analysis Sets and Annotations7-17All Spots in MemberThe All spots in member option will create an analysis set containing all the spots in a selected

PDQuest User Guide7-183. Spots that are unique to set A plus spots that are unique to set B.4. Spots that are found only in set A.5. Spots that are fo

Analysis Sets and Annotations7-19Fig. 7-8. Boolean Analysis SetEnter the name and description to be given to the analysis set. In the Compare section,

PDQuest User Guide7-20As with all other types of analysis sets, when the Analysis Set Template is open, you can view the results in the MatchSet immed

Analysis Sets and Annotations7-21Fig. 7-9. Matching Analysis Set There are two types of Matching analysis sets. The first option, Spots matched to eve

PDQuest User Guide7-22specify the spot marker, on which gel(s) to show the spots, and what information to show on the gel(s). When you open the Analys

PDQuest User Guide1-12The HSK can be inserted at any point in the ADB path—between the computer and the keyboard, between the keyboard and the mouse,

Analysis Sets and Annotations7-23Fig. 7-10. Annotation Tool.To open the tool with spot(s) selected, select Annotation Select Tool from the Analysis me

PDQuest User Guide7-247.2.b Annotation CategoriesAnnotations are organized in categories. Some examples of annotation categories are protein name, ami

Analysis Sets and Annotations7-25should be selected. You can also create specialized categories using the URL arg and Filename buttons (category types

PDQuest User Guide7-26File Name CategoriesThis type of category provides a link between spots and files on the user’s computer, network, or removable

Analysis Sets and Annotations7-27 Protein Name CategoryYou can create a special category for identifying spots by their protein names instead of by SS

PDQuest User Guide7-287.2.e Entering an AnnotationAfter you have selected an annotation category and a spot or multiple spots, type the annotation in

Analysis Sets and Annotations7-29Fig. 7-13. Import Annotations ToolSelect a file to import by clicking the folder icon to the right of the field. The

PDQuest User Guide7-30 Fig. 7-14. Confirm Overwrite DialogIf you do not want to overwrite what is there already, click no and the import will skip tha

Analysis Sets and Annotations7-31Click Import when you are ready to import your annotations. A progress box appears indicating the number of additions

PDQuest User Guide7-32Fig. 7-16. Annotation Tool in reviewing mode.Highlight Target Spot will highlight the spot(s) that are selected in the Annotatio

Introduction1-131.8 Software LicenseWhen the software opens for the first time, you will see a Software License screen that shows the current status o

Analysis Sets and Annotations7-337.3 Browsing AnnotationsYou can click on an annotated spot in PDQuest and open an HTML page displaying all the annota

PDQuest User Guide7-34If you have created an annotation link for the spot in a URL category (see section 7.2.b, Annotation Categories), that link will

Analysis Sets and Annotations7-35Fig. 7-18. Create Annotation from Analysis Set dialog box.In Step 1, select the analysis set from the pulldown menu.

PDQuest User Guide7-367.5 Printing AnnotationsThe functions for printing spot annotations are located on the Print Annotations submenu of the Analysis

Analysis Sets and Annotations7-37Printing Annotations for All SpotsAll Spots, Specify Categ’s prints selected annotation categories for all the annota

PDQuest User Guide7-38Fig. 7-20. Transferring annotations.Select the member MatchSet that you want to transfer to using the To MatchSet pulldown list.

8-18. Basic Excision ToolThe Basic Excision Tool is used to control Bio-Rad’s ProteomeWorks Spot Cutter system for basic spot cutting operations. If y

PDQuest User Guide8-2Fig. 8-1. Basic Excision Tool dialog.The Basic Excision Tool includes a window for viewing the spot cutter camera image and a con

Basic Excision Tool8-3Fig. 8-2. Spot cutter setup8.1.a Focus Cutter CameraNote: If you are using a lens filter, make sure that it is installed before

PDQuest User Guide8-4Click on Lower Tip to drop the cutting tip to its lowest position. In this position, manually adjust the cutting tip height as de

PDQuest User Guide1-14Fig. 1-10. Software License Registration Form.Fill out the information in the Software License Registration Form. Be sure to ent

Basic Excision Tool8-5Specify the diameter of the cutting tip by selecting 1.0 mm or 1.5 mm. Note that the cut request circles that you make on the im

PDQuest User Guide8-6Wash Station 1 positionCalibrate the position of Wash Station 1 on the cutting platform by following the steps described above fo

Basic Excision Tool8-7 Fig. 8-4. Spot cutter calibration step 2. Step 2: The third dialog requires the calibration template grid pattern supplied with

PDQuest User Guide8-8When calibration is complete, you can proceed with normal use of the spot cutter. Once the cutter is calibrated, you do not need

Basic Excision Tool8-9Fig. 8-5. Light settings.If UV light is selected, specify an exposure time in seconds in the field. Also, make sure that the UV

PDQuest User Guide8-10Fig. 8-6. Transform window with Coomas color selected.The colored box displayed on the image shows the boundary of the cutting a

Basic Excision Tool8-11Spots selected outside the cutting area cannot be cut. Either remove the cut, or locate it inside the cutting area.8.2.b Step

PDQuest User Guide8-12If this is the first cut added, the Enter Plate Information dialog box will open first. when all the pertinent information is ad

Basic Excision Tool8-13Multiple Cuts of the Same SpotYou can make multiple cuts of the same spot. The cuts can be placed in separate microtiter plate

PDQuest User Guide8-14Fig. 8-10. Multiple cuts to be placed in the same well.Note: If the box you create contains too few cutting circles, simply drag

Introduction1-15simply open normally. Go to the Help menu and select Register to open the Software License screen.)Registering by Fax or E-mailIf you

Basic Excision Tool8-158.2.c Step 3. Set Cutter OptionsBefore beginning a cut run using the Basic Excision Tool, you must select the cutter options f

PDQuest User Guide8-16Fig. 8-11. Cuts being made. Confirming CutsFor visible spots, inspect the gel to confirm that each cut is being made correctly.F

Basic Excision Tool8-17Fig. 8-12. Confirmation image; note that the first cut made incorrectly.When you have confirmed that the cuts are being made in

PDQuest User Guide8-18Fig. 8-13. Specify the wells to re-cut.In the pop-up box, enter the numbers of your recut requests (microplate number, well numb

Basic Excision Tool8-19Fig. 8-14. Confirm cuts window.Step 1: Answer "Yes" to bring up the following on-screen instructions for imaging the

PDQuest User Guide8-20Step 3: Place a clean plastic Gel Sheet on top of the gelStep 4: Place the microtiter plate on top of the plastic sheet. Note th

Basic Excision Tool8-21Fig. 8-17. Microtiter plate after zoom and transform functions applied.Step 8: If any of the wells are empty and you want to re

PDQuest User Guide8-22Step 10: Remove the plastic sheet from the top of the gel.Step 11: Do not move the gel. The image and spot selections that were

Basic Excision Tool8-238.2.g Saving the ImageTo save the image taken by the spot cutter, click the Save button in the Basic Excision Tool window. You

PDQuest User Guide8-24

PDQuest User Guide1-16Once you have typed in the correct password, the OK light next to the password field will change to green and the Enter button w

9-19. Integrated Excision ToolThe Integrated Excision Tool allows you to cut spots that have been matched in a MatchSet and placed in an analysis set

PDQuest User Guide9-29.1 Excision Gel SelectionThe Excision Gel Selection tool is used to select the gel(s) in a MatchSet from which to cut spots usin

Integrated Excision Tool9-3Fig. 9-2. Excision Gel Selection.9.1.a Step 1. Select Analysis SetSelect the analysis set you want to cut from the pop-up

PDQuest User Guide9-4in the different gels in the MatchSet. The first spot in the set is magnified and highlighted in each of the gels of the MatchSet

Integrated Excision Tool9-5Fig. 9-3. Excision Gel selection, Step 2.9.1.b Step 2. Set Selection ModeIn this step, you can select parameters for autom

PDQuest User Guide9-6Select the Auto-select option to automatically select the best gels to cut from based on spot quantity and quality. When you choo

Integrated Excision Tool9-7gels, the rows are spots. You can use this table to make cut requests or modify the auto-selection of cuts.Under Table Opti

PDQuest User Guide9-8The spots selected to be cut are highlighted in the table in blue. The table will initially show one cut request per spot—that is

Integrated Excision Tool9-9Fig. 9-4. Select Microtiter Plate pop-ups.The Select Microtiter Plate pop-up prompts you to specify the plate number and si

PDQuest User Guide9-10would load your spots from one MatchSet/analysis set on the plate, then select a different MatchSet/analysis set, skip the previ

PDQuest User GuideiiBio-Rad Technical Service DepartmentPhone: 800-424-6723 510-741-2612Fax: 510-741-5802E-mail: [email protected] Notice: N

Introduction1-17have a purchase order number or software serial number, and can leave these fields blank) and click on Submit Via Internet.A free tria

Integrated Excision Tool9-11Manually adjust the camera lens and position as described in the hardware manual to optimize the image. When you are satis

PDQuest User Guide9-12Fig. 9-5. Spot cutter settings dialog box.In the dialog box, select the communications port to the spot cutter by clicking on CO

Integrated Excision Tool9-13Well A1 positionThe fields and buttons in this section are used to calibrate the position of the microplate for proper loa

PDQuest User Guide9-14Note: If you are using the lens filter for UV light, make sure that it is installed BEFORE calibration. If you add or remove the

Integrated Excision Tool9-15been previously installed on the cutter. Make sure the grid is flat and aligned with the stage edges. Click Ready to proce

PDQuest User Guide9-16Fig. 9-7. Integrated excision tool.1. Select the Cut List. In this step, you select the cut list created using the Excision Gel

Integrated Excision Tool9-17Step 1. Select the Cut ListAt the top of the Integrated Excision Tool dialog, click the pulldown button to select from the

PDQuest User Guide9-18Select the wash stations to use after each cut by clicking on one or more checkboxes (Station 1, Station 2, etc.).Under Misc. Op

Integrated Excision Tool9-19Step 4. Align Analysis and Cutter ImagesAfter you have selected the cut list and the cut run settings, click the Align but

PDQuest User Guide9-20Step 3: Perform alignment.In Step 3, you will have the option of skipping auto-alignment by making the software work in totally

PDQuest User Guide1-18Phone: 800-424-6723 (in the U.S.)+1-510-741-6996 (outside the U.S.)

Integrated Excision Tool9-21Note: You always have the option of manually correcting spot positions. Auto-alignment is not always correct and the manua

PDQuest User Guide9-22Note: For UV exposures, there will be a 15-second delay while the lamps heat up before the exposure begins.The camera will take

Integrated Excision Tool9-23If spots in the cutter image have not aligned correctly with corresponding spots in the analysis image, make sure the scan

PDQuest User Guide9-24camera image to the correct position. Note that you can in fact drag any spot on the camera image any time to manually correct i

Integrated Excision Tool9-25Cut Area displays a green box on the cutter camera image; this shows the boundary of the cutting area. The cutting head ca

PDQuest User Guide9-26Fig. 9-15. Cutting progress.As each cut is being made, it will be highlighted in the table list. In progress or Completed displa

Integrated Excision Tool9-27Fig. 9-16. Progress completed on six cuts in the cut run.Confirming Cuts The Confirm button helps you check the cut progre

PDQuest User Guide9-28 Switching GelsWhen all the spots on one gel have been cut, you will be prompted to place the next gel on the spot cutter platfo

Integrated Excision Tool9-29Fig. 9-17. Confirm cuts window.Step 1: Answer "Yes" to bring up the following on-screen instructions for imaging

PDQuest User Guide9-30Step 3: Place a clean plastic Gel Sheet on top of the gelStep 4: Place the microtiter plate on top of the plastic sheet. Note th

2-12. General Operation2.1 Graphical Interface2.1.a Menu BarPDQuest has a standard menu bar with pulldown menus that contain all the major features an

Integrated Excision Tool9-31Fig. 9-20. Microtiter plate after zoom and transform functions applied.Step 8: If any of the wells are empty and you want

PDQuest User Guide9-32Step 10: Remove the plastic sheet from the top of the gel.Step 11: Do not move the gel. The image and spot selections that were

Integrated Excision Tool9-339.2.d Exporting the Cut ListYou can export the information in the cut list as a spreadsheet file. Click the Export button,

PDQuest User Guide9-34

10-110. Mass Spectrometry AnalysisAfter you have cut spots from a gel using the Integrated Excision Tool and digested them, you can select the paramet

PDQuest User Guide10-2Step 1In the dialog box, the MatchSet name is listed next to MatchSet. Select the cut list you want to analyze from the Cut List

Mass Spectrometry Analysis10-3Select the processing parameters using the Processing Parameters pulldown list.You can specify a mass spec run number in

PDQuest User Guide10-4In Step 3, the samples in the selected run are listed by microtiter plate well and sample date. Click on a sample to select it.I

Mass Spectrometry Analysis10-5Fig. 10-1. Example of the Hit Table annotation category and entries.In addition, the protein name is included in the sta

PDQuest User Guide10-6Fig. 10-2. Mass Spec Score Overlay dialog.In the dialog box, indicate the instrument you want to report scores for by selecting

PDQuest User Guide2-2• Identification—Excision (Spot cutting) and Mass Spectrometry analysis tools.• Reports—Graphs and Reports. Print and Export.• Wi

Mass Spectrometry Analysis10-7With your MatchSet open, select Protein Probe from the Identification menu and click on a spot for which you’ve imported

PDQuest User Guide10-8Fig. 10-3. Import Mascot resultsSet Search FiltersIn this step of the Import Mascot Results... dialog, select your search filter

Mass Spectrometry Analysis10-9The Replace Existing data without confirmation check box allows you the option of overwriting current data. If this box

PDQuest User Guide10-10Fig. 10-4. Peptide Mass Fingerprint Search dialogFor example, a data file created in the Generate Mass Lynx Worksheet dialog mi

Mass Spectrometry Analysis10-11Highlight the desired search and the list of hits automatically appear in the Search results field. Click Mascot Search

PDQuest User Guide10-12

11-111. Graphs and ReportsThis chapter describes the graphs and reports found in PDQuest. While most of the graphs and reports described in this secti

PDQuest User Guide11-2Fig. 11-2. Configure Graphs toolTo select a graph configuration, highlight the desired configuration and click Apply. The tool c

Graphs and Reports11-3Fig. 11-3. Editing a ConfigurationStep 1: Enter a name and description in the requisit fields. Step 2: Next, select whether you

PDQuest User Guide11-4Fig. 11-4. Colorized graphs showing replicate group by individual and groupTo delete a configuration, highlight the item you wis

General Operation2-32.1.c Status BoxesThere are two status boxes in PDQuest. These appear to the right of the main toolbar.The first box displays any

Graphs and Reports11-511.2.a Data Displayed in the HistogramEach bar in a histogram for a spot represents the spot’s quantity in a member of a MatchSe

PDQuest User Guide11-6Fig. 11-7. Sample histogram with Replicate Group Quantitation.11.2.b Types of GraphsSpot Review ToolSpot Review Tool on the Anal

Graphs and Reports11-7Column GraphsColumn Graph on the Reports menu and toolbar will fill the right and left margins with histograms of spots in the M

PDQuest User Guide11-8Select A-B Overlay from the Reports menu and click the Master of the MatchSet in which you want to perform the comparison. A pop

Graphs and Reports11-911.4 Quantity Table ReportIf you select Quantity Table Report from the Report menu, the Quantity Table Report dialog box opens.F

PDQuest User Guide11-10Specify the spots to include in your report: All Matched Spots or the spots in a Specified Analysis Set dropdown list. If you c

Graphs and Reports11-11Once you have selected your options, click Done to open the report viewer.Fig. 11-10. Viewing a Quantity Table ReportThe report

PDQuest User Guide11-12Fig. 11-11. Quantity Graph Report dialog box.You can type a report title, the name of the researcher, and the name of the resea

Graphs and Reports11-13Fig. 11-12. Quantity Graph Report ViewerThe report viewer allows you the option of printing or reformatting the report. Click r

PDQuest User Guide11-14In the Master Image dialog, you can type in a report title, the name of the researcher, and the name of the research institutio

PDQuest User Guide2-4Fig. 2-3. Secondary toolbar formats and features.The expanded toolbar format shows the name of each of the commands. Click the Re

Graphs and Reports11-15Fig. 11-14. Scatter plot Report.When you select Scatter Plot Report from the Report menu, a dialog opens in which you can enter

PDQuest User Guide11-16Fig. 11-15. Scatter Plot Report ViewerThe report viewer allows you the option of printing or reformatting the report. Click the

A-1Appendix A Gel Doc 2000Fig. A-1. Gel Doc.Before you can begin acquiring images, the Gel Doc system must be properly installed and connected with t

PDQuest User GuideA-2To use the Gel Doc, you will need to have the Bio-Rad-supplied acquisition board installed in your PC or Macintosh. The drivers f

Appendix A. Gel DocA-3Fig. A-2. Gel Doc acquisition windowThe Gel Doc video display window will open in “live” mode, giving you a live video display

PDQuest User GuideA-44. Optimize the display.5. Analysis.6. Select the output.A.2 Step I. Position GelThe Gel Doc window will open in “live” mode, giv

Appendix A. Gel DocA-5focusing on, you can place a ruler in the Gel Doc cabinet so that it is visible in the image.A.3 Step II. Select Image ModeThe I

PDQuest User GuideA-6Note: If you know the approximate exposure time you want (± 3 seconds), you can skip this step and go directly to Manual Expose.

Appendix A. Gel DocA-7Fig. A-5. Manual Expose.With Manual Expose activated, you can adjust the exposure time directly by changing the number of secon

PDQuest User GuideA-8Note: Freeze is automatically activated if you adjust any of the subsequent controls (e.g., Video Print, Image Mode, Display cont

General Operation2-5Fig. 2-4. PDQuest Quick GuideIn the expanded format, the Quick Guide commands are numbered as well as named, so that the order of

Appendix A. Gel DocA-9Gamma SliderSome images may be more effectively visualized if their data are mapped to the computer screen in a nonlinear fashio

PDQuest User GuideA-10AnnotateClicking on Annotate will open a separate image window displaying the captured image. The default name for the image wil

Appendix A. Gel DocA-11bottom of the printout by selecting the appropriate checkboxes in the Options dialog box. (See section A.9, Options.)SaveClicki

PDQuest User GuideA-12Fig. A-9. Available options in the Gel Doc acquisition window.Click on OK to implement any changes you make in this box. Clicki

Appendix A. Gel DocA-13as white in the image, while the maximum slider defines the pixel value that will appear as black. The slider scale is 0–255, w

PDQuest User GuideA-14With this checkbox selected, when you save a scan, a backup copy will be placed in the same directory as the scanned image. Wind

B-1Appendix B ChemiDocFig.B-1. ChemiDoc.Before you can begin acquiring images, the ChemiDoc system must be properly installed and connected with the h

PDQuest User GuideB-2To use the ChemiDoc, you will need to have the Bio-Rad-supplied acquisition board installed in your PC or Macintosh. The drivers

Appendix B. ChemiDocB-3Fig.B-2. ChemiDoc acquisition windowThe ChemiDoc video display window will open in “live” mode, giving you a live video display

PDQuest User GuideB-44. Optimize the display.5. Analysis.6. Select the output.B.2 Step I. Position GelThe ChemiDoc window will open in “live” mode, gi

PDQuest User Guide2-6Fig. 2-5. Keyboard Layout.The pulldown menus also list the shortcut keys for the menu commands.Note: Mouse-assignable commands be

Appendix B. ChemiDocB-5focusing on, you can place a ruler in the ChemiDoc cabinet so that it is visible in the image.B.3 Step II. Image ModeThe Image

PDQuest User GuideB-6exposure based on the number of saturated pixels in the image, you can enter a specific exposure time, or you can take a series o

Appendix B. ChemiDocB-7At this point, if you are in UV or White image mode, Manual Expose will be automatically activated. If you are in Chemi mode, t

PDQuest User GuideB-8Once you are satisfied with the quality of the displayed image, click on the Freeze button to stop the exposure process. The last

Appendix B. ChemiDocB-9Fig.B-7. Live Acquire settings.Note: You should specify no more than 10 exposures in the Live Acquire Settings dialog, to avoid

PDQuest User GuideB-10To stop the Live Acquire, click on the Freeze button or adjust any of the subsequent controls (e.g., Video Print, Image Mode, Di

Appendix B. ChemiDocB-11UV mode, dragging the High slider handle to the left will make weak signals appear brighter. Dragging the Low slider handle to

PDQuest User GuideB-12B.6 Step V. AnalysisThe Analysis step of the ChemiDoc acquisition window allows you to add annotations and analyze the newly acq

Appendix B. ChemiDocB-13Video PrintClicking on Video Print will automatically send the currently displayed frame (either live or integrated) to a vide

PDQuest User GuideB-14Fig.B-10. Available options in the ChemiDoc acquisition window.Click on OK to implement any changes you make in this box. Clicki

General Operation2-7click the mouse button once, the defined region is magnified and the tool is automatically deassigned from your mouse.2.3 File Com

Appendix B. ChemiDocB-15These sliders may be used to adjust the minimum and maximum voltage settings of your video capture board. The minimum slider d

PDQuest User GuideB-16Save OptionsTo automatically create a backup copy of any scan you create, select the Make Backup Copy checkbox.With this checkbo

Appendix B. ChemiDocB-17To change the acquisition window to Simple Acquisition Mode, check the box marked Simple Acquisition Mode. The change will tak

PDQuest User GuideB-18

C-1Appendix C ChemiDoc XRSFig.C-1. ChemiDoc XRS.Before you can begin acquiring images, the ChemiDoc XRS system must be properly installed and connecte

PDQuest User GuideC-2To use the ChemiDoc XRS, you will need to have the Bio-Rad-supplied acquisition board installed in your PC or Macintosh. The driv

Appendix C. ChemiDoc XRSC-3Fig.C-2. ChemiDoc XRS acquisition windowWhen the ChemiDoc XRS window first opens, no image will be displayed.The control pa

PDQuest User GuideC-4C.2 Step I. Select ApplicationTo set the appropriate parameters for the type of object you are imaging, click on the Select butto

Appendix C. ChemiDoc XRSC-5Selecting a higher Gain setting (2x) provides higher sensitivity without reduced resolution; however, noise will also incre

PDQuest User GuideC-6C.4 Step III. Acquire ImageThe ChemiDoc XRS control panel has several features for creating image exposures. You can take an auto

PDQuest User Guide2-8A MatchSet can consist of one gel or many gels, depending on the type and size of the experiment. The MatchSet is displayed in a

Appendix C. ChemiDoc XRSC-7Once an image has reached the specified percentage of saturated pixels, it is captured and displayed in the video display w

PDQuest User GuideC-8Fig.C-7. Freezing the manual exposure.Live AcquireLive Acquire mode allows you to specify an interval over which a series of prog

Appendix C. ChemiDoc XRSC-9fewer the exposures, the less background will be added to the image. See the Release Notes for additional instructions on r

PDQuest User GuideC-10To enable this feature, select the Flat Fielding checkbox.UV Illumination Flat Fielding: When you first select the Flat fielding

Appendix C. ChemiDoc XRSC-11Fig.C-10. Using the saved reference image.Note: Flat fielding is unavailable for White EPI illumination and chemiluminesce

PDQuest User GuideC-12Fig.C-11. Available options in the ChemiDoc XRS acquisition window.Click on OK to implement any changes you make in this box.C.5

Appendix C. ChemiDoc XRSC-13Note: If you are performing experiments that are longer than 5 minutes (e.g., chemiluminescence), this should be deselecte

PDQuest User GuideC-14C.5.d. Save OptionsTo automatically create a backup copy of any scan you create, select the Make Backup Copy checkbox.With this

Appendix C. ChemiDoc XRSC-15Highlight Saturated PixelsWhen this box is checked, any saturated pixels in the image will appear highlighted in red in th

PDQuest User GuideC-16

Table of Contentsiii1. Introduction ... 1-11.1. Overview of PDQuest ...

General Operation2-9Fig. 2-7. Example of a Scanset.A scanset consists of three separate images of the same gel image. They are displayed in subwindo

D-1Appendix D GS-700 Imaging DensitometerFig. D-1. GS-700 Imaging DensitometerBefore you can begin scanning images with the GS-700 Imaging Densitomet

PDQuest User GuideD-2instead of capturing real images, the window will create “dummy” images of manufactured data.You do not need to be connected to a

Appendix D. GS-700D-3Fig. D-2. GS-700 acquisition window.The scanning window is marked by grid lines that divide the area into square centimeters. Th

PDQuest User GuideD-4The control panel has been arranged from top to bottom to guide you through the acquisition procedure. There are four basic steps

Appendix D. GS-700D-5The applications are listed in a tree that expands from left to right. First you select the category of your application, then yo

PDQuest User GuideD-6Next to Filter, click on either the Red, Green, Blue, or White checkbox, or a combination of two of the first three (Red-Green, G

Appendix D. GS-700D-7Selecting an AreaUsing the preview scan as a guide, select your scan area by dragging your mouse within the scanning window. The

PDQuest User GuideD-8Fig. D-7. Select Scan Resolution dialog box.Available resolutions are listed from highest to lowest in terms of the dimensions o

Appendix D. GS-700D-9Fig. D-8. Entering a custom resolution (with Oversample selected).Image File SizeImage File Size (under Select Resolution) shows

PDQuest User GuideD-10D.6 CalibrationIf you have installed a calibration overlay, you can automatically calibrate your transmissive and reflective sca

PDQuest User Guide2-10Analysis SetAn Analysis set is a set of spots you have chosen to study. Analysis sets allow you to create groups of spots that a

Appendix D. GS-700D-11Calibration Strip WindowWhen calibration is turned on, a calibration strip window will appear below the main scanning window and

PDQuest User GuideD-12Fig. D-10. Step Tablet dialog box.The dialog box will indicate whether the displayed form is for the transmissive or reflective

Appendix D. GS-700D-13Finally, enter the values in the appropriate fields under the Diffuse column. After the step tablet is scanned, the software wil

PDQuest User GuideD-14D.6.b Calibration SettingsAfter you have entered the step tablet values, you can immediately calibrate by clicking on the Calibr

Appendix D. GS-700D-15Auto Save After ScanTo automatically save any scan you create, click on the Auto Save After Scan checkbox.With this checkbox sel

PDQuest User GuideD-16

E-1Appendix E GS-710 Imaging DensitometerFig. E-1. GS-710 Imaging DensitometerBefore you can begin scanning images with the GS-710 Imaging Densitomete

PDQuest User GuideE-2instead of capturing real images, the window will create “dummy” images of manufactured data.You do not need to be connected to a

Appendix E. GS-710E-3Fig. E-2. GS-710 acquisition windowThe scanning window is marked by grid lines that divide the area into square centimeters. Thes

PDQuest User GuideE-4The control panel has been arranged from top to bottom to guide you through the acquisition procedure. There are five basic steps

General Operation2-11Fig. 2-9. Open dialog box.In the PDQuest Open dialog box:• Already open images are marked with an asterisk.• File types and icons

Appendix E. GS-710E-5Fig. E-3. Example of the application tree in the GS-710 dialog box.The applications are listed in a tree that expands from left t

PDQuest User GuideE-6Choosing Your Own SettingsIf you know the filter and light source settings you want, or want to experiment with different setting

Appendix E. GS-710E-7E.3 Step II. Select Scan AreaPreview ScanBefore selecting the particular area to scan, you can preview the entire scanning area t

PDQuest User GuideE-8E.4 Step III. Select ResolutionTo select from a list of possible scanner resolutions, click on the Select button under Select Res

Appendix E. GS-710E-9Specifying Your Own ResolutionIf you select Oversample under More Options, you can specify your own resolution within the range o

PDQuest User GuideE-10To set the automatic calibration settings, click on the More Options button in the GS-710 acquisition window. This will open the

Appendix E. GS-710E-11Note: Scanning in transmissive mode with incorrect step tablet values entered into the computer can cause significant errors in

PDQuest User GuideE-12Next, enter the values for the transmissive step tablet in the appropriate fields under the Diffuse column. After the step table

Appendix E. GS-710E-13E.5.b Calibration SettingsAfter you have entered the step tablet values, you can immediately calibrate by clicking on the Calibr

PDQuest User GuideE-14E.7 Other OptionsOversampleThis feature allows you to scan at the maximum resolution of the GS-710 (42.3 x 42.3 microns) and the

PDQuest User Guide2-12or down arrow to the right of the field to display a hierarchical tree structure locating the default drive, folder and file.Not

Appendix E. GS-710E-15Highlight Saturated PixelsWhen this box is checked, any saturated pixels in the image will appear highlighted in red in the scan

PDQuest User GuideE-16

F-1Appendix F GS-800 Imaging DensitometerFig.F-1. GS-800 Imaging DensitometerBefore you can begin scanning images with the GS-800 Imaging Densitometer

PDQuest User GuideF-2you have a PC with a Windows 98 or Windows ME operating system, you may also need to load the SCSI and WinASPI drivers that came

Appendix F. GS-800F-3Fig. F-2. GS-800 acquisition windowThe scanning window is marked by grid lines that divide the area into square centimeters. Thes

PDQuest User GuideF-4The control panel has been arranged from top to bottom to guide you through the acquisition procedure. There are five basic steps

Appendix F. GS-800F-5Fig. F-3. Example of the application tree in the GS-800 dialog box.The applications are listed in a tree that expands from left t

PDQuest User GuideF-6Choosing Your Own SettingsIf you know the filter and light source settings you want, or want to experiment with different setting

Appendix F. GS-800F-7F.3 Step II. Select Scan AreaPreview ScanBefore selecting the particular area to scan, you can preview the entire scanning area t

PDQuest User GuideF-8F.4 Step III. Select ResolutionTo select from a list of possible scanning resolutions, click on the Select button under Step III.

General Operation2-132. 16-bit Grayscale. Bio-Rad’s Molecular Imager (storage phosphor) systems use 16-bit pixel values to describe intensity of scale

Appendix F. GS-800F-9Fig. F-8. Entering a custom resolution (with Oversample selected).Image File SizeThe size of the scan file for the selected resol

PDQuest User GuideF-10Fig. F-9. Densitometer Options dialog box.Note that calibration is always on for the GS-800.F.5.a Step Tablet ValuesThe built-in

Appendix F. GS-800F-11Fig. F-10. Step Tablet dialog box.Attached to the outside of your GS-800, you will find a copy of the manufacturer’s printout of

PDQuest User GuideF-12Reflective Step TabletFor the reflective step tablet, it is recommended that you use the default target values in the software.

Appendix F. GS-800F-13F.5.b Other Calibration SettingsAfter you have entered the step tablet values, you can immediately calibrate by clicking on the

PDQuest User GuideF-14F.7 Other OptionsOversampleThis feature allows you to scan at the maximum resolution of the scanner and then use spatial averagi

Appendix F. GS-800F-15Highlight Saturated PixelsWhen this box is checked, any saturated pixels in the image will appear highlighted in red in the scan

PDQuest User GuideF-16

G-1Appendix G Fluor-S MultiImagerFig.G-1. Fluor-S MultiImager.Before you can begin acquiring images using the Fluor-S® MultiImager, the imaging system

PDQuest User GuideG-2PC Only: A Note About SCSI CardsThe Fluor-S is connected to your computer by a Small Computer System Interface (SCSI) cable. To u

PDQuest User Guide2-14Fig. 2-10. Export to TIFF dialog.Note: See Filtered Images and Gaussian Images for a description of the different image types.In

Appendix G. Fluor-SG-3Fig.G-2. Fluor-S acquisition windowWhen the Fluor-S window first opens, no image will be displayed.The control panel has been ar

PDQuest User GuideG-4G.2 Step I. Select ApplicationTo set the appropriate filter and other parameters for the type of object you are imaging, click on

Appendix G. Fluor-SG-5Custom ApplicationsIf your application is not listed, if you want to use a user-installed filter, or if you want to access High

PDQuest User GuideG-6Scan DimensionIf an application uses trans illumination, the Scan Dimension buttons become active. The scan dimension is the dist

Appendix G. Fluor-SG-7PositionAfter you have selected your application, you are ready to center your gel or other object within the camera frame. To d

PDQuest User GuideG-8G.4 Step III. Set Exposure TimeWhen you are ready to capture an image, you will need to select an exposure time. “Exposure” refer

Appendix G. Fluor-SG-9For most applications, you can select an exposure time, capture an image, study it, then adjust the exposure time accordingly. R

PDQuest User GuideG-10A preview scan takes only half as long to create as a real scan, because the preview scan does not capture a “dark” image (see t

Appendix G. Fluor-SG-11After an image has been acquired, a separate window will pop up containing the new image. The window will have a default file n

PDQuest User GuideG-12Fig.G-9. Options dialog box.G.6.a Dark Subtraction TypeAll CCD cameras accumulate electrons that produce a signal that is indist

General Operation2-15The Analysis option exports the image data unmodified by any viewing adjustments you may have made (such as Transform or Zoom). I

Appendix G. Fluor-SG-13ReferencedIf you do not want to perform a dark exposure with each acquisition, you can take a “reference” dark exposure that wi

PDQuest User GuideG-14A pop-up box will prompt you to enter a new reference dark exposure time in seconds. Click on OK to implement your change. The n

Appendix G. Fluor-SG-15root name appended by a number indicating the exposure sequence. The final, full exposure will have the root name only, with no

PDQuest User GuideG-16When you change one imaging area dimension, the other will change to maintain the aspect ratio of the camera lens.The imaging ar

Appendix G. Fluor-SG-17Highlight Saturated PixelsWhen this box is checked, any saturated pixels in the image will appear highlighted in red in the sca

PDQuest User GuideG-18

H-1Appendix H Fluor-S MAX MultiImagerFig.H-1. Fluor-S MAX MultiImager.Before you can begin acquiring images using the Fluor-S® MAX MultiImager, the im

PDQuest User GuideH-2PC Only: A Note About SCSI CardsThe Fluor-S MAX is connected to your computer by a Small Computer System Interface (SCSI) cable.

Appendix H. Fluor-S MAXH-3Fig.H-2. Fluor-S MAX acquisition window.When the Fluor-S MAX window first opens, no image will be displayed.The control pane

PDQuest User GuideH-4H.2 Step I. Select ApplicationTo set the appropriate filter and other parameters for the type of object you are imaging, click on

PDQuest User Guide2-16if this action is not executable. If the action is executable you will be prompted to confirm. File > Close (Alt F4) closes t

Appendix H. Fluor-S MAXH-5Custom ApplicationsIf your application is not listed, if you want to use a user-installed filter, or if you want to access U

PDQuest User GuideH-6Scan DimensionIf an application uses trans illumination, the Scan Dimension buttons become active. The scan dimension is the dist

Appendix H. Fluor-S MAXH-7H.3 Step II. Position/FocusNote: When you click on the Position or Focus button, the light inside the Fluor-S MAX box automa

PDQuest User GuideH-8more accurately focus the camera. Then, after focusing, increase the f-stop to the desired setting.After you have positioned your

Appendix H. Fluor-S MAXH-9For most applications, you can select an exposure time, capture an image, study it, then adjust the exposure time accordingl

PDQuest User GuideH-10A preview scan takes only half as long to create as a real scan, because the preview scan does not capture a “dark” image (see b

Appendix H. Fluor-S MAXH-11After an image has been acquired, a separate window will pop up containing the new image. The window will have a default fi

PDQuest User GuideH-12Fig.H-10. Options dialog box.H.6.a Dark Subtraction TypeAll CCD cameras accumulate electrons that produce a “signal” that is ind

Appendix H. Fluor-S MAXH-13ReferencedIf you do not want to perform a dark exposure with each acquisition, you can take a “reference” dark exposure tha

PDQuest User GuideH-14A pop-up box will prompt you to enter a new reference dark exposure time in seconds. Click on OK to implement your change. The n

General Operation2-172.3.g Image InfoOn the main toolbar, Image> Image Info displays general information about your image, including the scan date,

Appendix H. Fluor-S MAXH-15root name appended by a number indicating the exposure sequence. The final, full exposure will have the root name only, wit

PDQuest User GuideH-16The imaging area will change depending on your zoom factor. For example, if you have zoomed in on a area that is 4.5 x 3.5 cm, t

Appendix H. Fluor-S MAXH-17File Size of ImagesImage File Size (below Options) shows the size of the image file you are about to create. This size is d

PDQuest User GuideH-18

I-1Appendix I Personal Molecular Imager FXFig.I-1. Personal Molecular Imager FXBefore you can begin acquiring images using the Personal Molecular Imag

PDQuest User GuideI-2PC Only: A Note About SCSI CardsThe Personal FX is connected to your computer by a Small Computer System Interface (SCSI) cable.

Appendix I. Personal FXI-3Fig.I-2. Personal FX acquisition windowThe default scanning window is marked by grid lines that divide the area into quadran

PDQuest User GuideI-42. Select the resolution3. Acquire the imageI.2 Step I. Select Scan AreaTo select a scan area, drag your mouse within the scannin

Appendix I. Personal FXI-5You can also select the scanning area by entering coordinates in the appropriate fields (Top, Bottom, Left, Right). After yo

PDQuest User GuideI-6File Size of ImagesImage File Size (below Select Resolution) shows the size of the scan file you are about to create. If you do n

PDQuest User Guide2-18changes made to the image including the date the changes were made. To print the file information, click Print.2.3.h Reduce File

Appendix I. Personal FXI-7I.5 OptionsAuto Save After ScanTo automatically save any scan you create, click on the Auto Save After Scan checkbox.Note: I

PDQuest User GuideI-8Disable Default FilterTo disable the default filter in the FX, click the Disable Default Filter checkbox.Warn on Saturated Pixels

J-1Appendix J Molecular Imager FX Family (FX Pro, FX Pro Plus and Molecular FX)Fig. J-1. Molecular Imager FXBefore you can begin acquiring images usin

PDQuest User GuideJ-2Note: The FX should be turned on and the initialization sequence completed before the host computer is turned on (except in the c

Appendix J. FXJ-3Fig. J-2. FX acquisition windowThe default scanning window is marked by grid lines that divide the area into quadrants. There is also

PDQuest User GuideJ-43. Select the resolution.4. Acquire the image.J.2 Step I. Select ApplicationIn Step 1, you select the appropriate filters and oth

Appendix J. FXJ-5Fig. J-3. Enabling Channel 2.Enabled channels have a green check mark on their tabs.You do not need to enable Channels 2–4 in sequenc

PDQuest User GuideJ-6Fig. J-4. Example of an application tree: Ethidium Bromide gel.Standard ApplicationsThe standard applications and associated sett

Appendix J. FXJ-71Not supported in the FX Pro and FX Pro Plus systems.First select your general application, next select the particular stain or mediu

PDQuest User GuideJ-8Sample IntensityMany FX applications require that you select a sample intensity (High, Medium, or Low) from the application tree.

PDQuest User Guideiv3.4. Tiling Windows ... 3-43.5. Magn

General Operation2-19Fig. 2-12. Reduce File Size dialog box, before and after pixel size increase.Note: Asymmetric pixel reduction (i.e., making pixel

Appendix J. FXJ-9To select a filter (including user-defined) or filter combination, click on the buttons for Filters A, B, and C, and make your choice

PDQuest User GuideJ-10Finally, enter a name for your application in the Name field and click on OK to implement your changes.After you have created an

Appendix J. FXJ-11 ¢            J.3 Step II. Select Scan AreaTo select

PDQuest User GuideJ-12You can also select the scanning area by entering coordinates in the appropriate fields (Top, Bottom, Left, Right). After you en

Appendix J. FXJ-13File Size of ImagesImage File Size (below Select Resolution) shows the size of the scan file you are about to create. If you do not

PDQuest User GuideJ-14J.6 OptionsAuto Save After ScanTo automatically save any scan you create, click on the Auto Save After Scan checkbox.With this c

Appendix J. FXJ-15Hide GridTo hide the gridlines in the scanning area window, click on the Hide Grid checkbox.Disable Default FilterTo disable the def

PDQuest User GuideJ-16

K-1Appendix K VersaDocFig.K-1. VersaDoc.Before you can acquire images using the VersaDoc Imaging System, you need to install the Roper Scientific inte

PDQuest User GuideK-2The CD also contains Roper Scientific camera interface driver installation instructions for Macintosh computers. See the VersaDo

PDQuest User Guide2-20If you choose to make a copy of the image, you will be asked to enter a name for the new copy before the operation is performed.

Appendix K. VersaDocK-31. Select the application.2. Position and focus the object to be imaged.3. Set the exposure time.4. Acquire the image.K.2 Step

PDQuest User GuideK-4Enabled channels are imaged sequentially. The separate scans are displayed and saved as separate images. The total imaging time d

Appendix K. VersaDocK-5Fig.K-3. The application tree in the VersaDoc acquisition window.Note: If you select an application that requires trans white i

PDQuest User GuideK-6Fig.K-4. Creating a new custom application.Enter a name for your application in the Name field.Next, click on the buttons next to

Appendix K. VersaDocK-7You can edit a custom application by selecting Custom, Edit, and the name of the application. You can also use this feature to

PDQuest User GuideK-8desired setting. See Table 1, “Recommended Exposure Times and Lenses,” on page 9.After you have positioned your sample, click on

Appendix K. VersaDocK-9The following table provides recommended exposure times for various applicationsTable 1: Recommended Exposure Times and LensesS

PDQuest User GuideK-10Note: For most applications, you can select an exposure time, capture an image, study it, and then adjust the exposure time acco

Appendix K. VersaDocK-11To enable this feature, select the Flat Fielding checkbox.Note: For applications using the UV or white light transillumination

PDQuest User GuideK-12Fig.K-6. Exposure Status bar when acquiring an image.Depending on which dark subtraction type you have selected under Options (s

General Operation2-212.5 Printing1. Page Setup opens a dialog box where you can select the size and source of your paper, portrait or landscape orien

Appendix K. VersaDocK-13Fig.K-7. Optimize Exposure dialog.Note: You should specify no more than 10 exposures in the Optimize Exposure dialog, to avoid

PDQuest User GuideK-14default base file name, the time stamp may change in the course of the series of exposures; in this case, the base file name wil

Appendix K. VersaDocK-15exposures. In most cases, you will want to subtract this dark current from your images.The settings for subtracting the dark c

PDQuest User GuideK-16Separate reference dark exposures will be taken for images that have different levels of binning or gain. Once you have created

Appendix K. VersaDocK-17K.6.b. SaveAuto Save After ScanTo automatically save any image you acquire using the Acquire button, click on the Auto Save Af

PDQuest User GuideK-18K.6.d. Auto-scale TransformAuto-scale Transform after Acquisition allows the user the option of having the image automatically p

L-1Appendix L Calibration and MergingYou can use calibration strips (calstrips) to calibrate your scans for more accurate quantitation. Calstrips are

PDQuest User GuideL-2Configuring Calstrip SubwindowsIf you are displaying multiple calstrips linked to multiple exposures (see section L.2, Merging Mu

Appendix L. TechniquesL-3Enter a title for the data record next to the Name prompt. You can enter descriptive information about the calstrip in the De

PDQuest User GuideL-4For example, you might begin with a 50 µg/ml stock solution of BSA and make segments of the calstrip starting at 50 µg and progre

PDQuest User Guide2-22Fig. 2-14. Print Image dialog box.In the General tab, select the printer and page range you want to use. In the Layout tab selec

Appendix L. TechniquesL-5 Fig. L-3. Gel Record Editor.Enter the date on which the gel was run in the text box next to the Gel run date prompt.Next to

PDQuest User GuideL-6Note: Most calibration problems arise from incorrectly entering the dates used to calculate radioactive decay factors for the iso

Appendix L. TechniquesL-7indicating that the calibration density decreases while the counts increase (or vice versa).To change the orientation of the

PDQuest User GuideL-8You can draw more boxes than the number of segments defined in the Calstrip Record. However, they are automatically and permanent

Appendix L. TechniquesL-9Calibration Curve ProblemsFind errant data points and their corresponding segments using the function Display Segment Quan.Ab

PDQuest User GuideL-10single gel should be the same since the same physical calibration strip was used to make each exposure.L.2 Merging Multiple Expo

Appendix L. TechniquesL-11Fig. L-5. Diagrammatic representation of merging.Cropping and Aligning Exposures of the Same Gel for Merging Before you can

PDQuest User GuideL-12

M-1Appendix M Cross-Platform File ExchangeIt is possible to move image data between Discovery Series software applications on different platforms. The

PDQuest User GuideM-2

General Operation2-23Select Print Actual Size from the File > Print submenu. The standard Print Image dialog box will open (see previous section).2

IndexIndex-1Numerics3D Viewer ... 3-18AA-B

Index-2PDQuest User GuideAnnotations ... 7-22B

IndexIndex-3CalstripsBoxing segments ... L-7Calibration cur

Index-4PDQuest User GuideVideo card ... B-2, C-2Video dis

IndexIndex-5Plot Density Distribution ... 3-12Plot Vertical Trace ...

Index-6PDQuest User GuideFinding spots ... 4-28F

IndexIndex-7GGaussian images ... 4-12Gaussian spots

Index-8PDQuest User GuideGraphs ... 11

IndexIndex-9Calibration step tablets ... F-10Filters and light source,

Index-10PDQuest User GuideAssigning to windows ... 3-3Closing ...

PDQuest User Guide2-24• The image title.• A description of the image if you specified one.• The directory location.• The filename of the image.• The t

IndexIndex-11LLandmarkingAuto-match after ... 2-43Landmarks

Index-12PDQuest User GuideShow Match ... 5-22Standard

IndexIndex-13NNormalization ... 6-23OOpening file

Index-14PDQuest User GuideToolbars ... 2-41Print

IndexIndex-15Rename ... 6-10ReportsA-B Compari

Index-16PDQuest User GuideSpot cutterBasic tool ...

IndexIndex-17Low quantity sets ... 4-25MrpI value ...

Index-18PDQuest User GuideThree by three (3x3) sections, viewing ... 3-10TIFF filesImpor

IndexIndex-19Exposure times, recommended ... K-9Gain ...

Index-20PDQuest User Guide

General Operation2-25Settings for the Mitsubishi P90W/P91W Video PrinterThere are three settings for the Mitsubishi P90W/P91W video printer. Set Contr

The Discovery Series™ Image Analysis Software Software License AgreementREAD THIS! THIS IS A LEGAL AGREEMENT BETWEEN YOU, THE CUSTOMER, AND BIO-RAD L

LIMITED WARRANTY AND REMEDIESBIO-RAD warrants the media on which the Program is furnished to be free from defects in materials and workmanship under n

SUCH PROGRAM EVEN IF BIO-RAD OR AN AUTHORIZED DEALER HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES, OR FOR ANY CLAIM BY ANY OTHER PARTY.SOME STA

PDQuest User Guide2-262.6.a Exporting an ImageTo export a Raw 2-D scan, Filtered image, or Gaussian image as a TIFF image, select Export to TIFF Image

General Operation2-27Analysis Export ModeThe Analysis option exports the image data unmodified by any viewing adjustments you may have made (such as T

PDQuest User Guide2-28Fig. 2-18. Status box confirms your export to TIFF is successful.2.6.b MatchSet DataData from a MatchSet can be exported as an

Contentsv5.2. Selecting the Master ... 5-95.3. Matching Spots

General Operation2-29Fig. 2-19. Exporting MatchSet data.In the dialog, you can export data for each gel in a MatchSet (Spot Data by Gel), or for each

PDQuest User Guide2-30The quantities of saturated spots can be estimated, reported as the value -3.0, or reported in some other way that you specify.

General Operation2-31Fig. 2-20. Spot data by group tab.Basic Export MatchSetThe Basic Export MatchSet dialog allows you to export the individual chara

PDQuest User Guide2-32Fig. 2-21. Export MatchSet Data dialog box.Next to the Data to export options, select the characteristic of the spot that you wa

General Operation2-33detected for the gel). Alternatively, it can be reported as (-1.0) or as a value that you enter in the text box next to the Speci

PDQuest User Guide2-34Fig. 2-22. Export Annotations pop-up box.Click an individual category name to select it, or shift-click or ctrl-click to select

General Operation2-352.7 PreferencesThe Preferences dialog box allows you to customize basic features of your system. Select Edit > Preferences to

PDQuest User Guide2-36Your institution name can be included in reports if you enter it in the Institute Name field.Under Windows, the Maximize applica

General Operation2-37Fig. 2-24. Path preferences Browse buttonTo set a particular file path, click the Browse button next to the path field and naviga

PDQuest User Guide2-38The MatchSets path Browse button connects to the main directory where you keep your MatchSet files. The Log path Browse button s

PDQuest User Guidevi8.3. Other Spot Cutter Controls ... 8-239. Integrated Ex

General Operation2-39The Micromass Install path sets the directory where your Micromass processing parameters are stored. This path is used to link to

PDQuest User Guide2-40If you want to apply a uniform background to Gaussian images so they more closely resemble the original gels, enter a background

General Operation2-412.7.d Toolbar PreferencesFig. 2-27. Toolbar preferencesClick the Toolbar tab to set the behavior and positioning of the secondary

PDQuest User Guide2-42The Placement Behavior setting determines whether a quick guide or toolbar will always pop up in the same place and format (Alwa

General Operation2-43Enter up to three letters for the MatchSet Name Prefix and a number for the MatchSet Name Sequence #.When you create a MatchSet,

PDQuest User Guide2-44Fig. 2-29. Imagers.The Edit > Preferences > Imagers tab contains a list of Bio-Rad imaging devices supported by the Discov

General Operation2-4511. Molecular Imager FXNote: If you check one or all of these devices they display in the File menu. You need to restart the prog

PDQuest User Guide2-46You can choose from up to four groups of mouse functions, and select either two or three buttons to assign to each group.type th

General Operation2-47Note: Some commands in PDQuest become mouse-assignable if you are displaying multiple subwindows. For example, if you select Spot

PDQuest User Guide2-48

ContentsviiAppendix E. GS-710 Imaging Densitometer ... E-1Appendix F. GS-800 Imaging Densitometer .

3-13. Viewing and Editing ImagesThis chapter describes the tools for displaying images in windows and subwindows, and magnifying and optimizing images

PDQuest User Guide3-2Fig. 3-1. Configuring the subwindows of a scanset.The Quick Config buttons immediately partition the subwindows into the configur

Viewing and Editing Images3-33.3 Assigning and Interchanging ImagesYou can use the Assign and Interchange commands to select the image you want to dis

PDQuest User Guide3-43.4 Tiling WindowsThe tile commands under the Window menu are used to arrange image windows on the screen.Note: The tile commands

Viewing and Editing Images3-5Fig. 3-3. Viewing functions on View menu and main toolbar.Zoom BoxUse the Zoom Box tool to magnify a specific region of

PDQuest User Guide3-6Fig. 3-4. Zoom Box tool.Zoom In/Zoom OutZoom In (Alt+F2, View menu and toolbar) will magnify an image, or all the images in a Ma

Viewing and Editing Images3-7Imitate ZoomImitate Zoom applies the magnification and positioning of a selected window or subwindow to all open windows

PDQuest User Guide3-8GrabUse this tool to drag the image in a window.Select Grab from the main toolbar or View menu, or position your cursor on the im

Viewing and Editing Images3-93.6.a Advanced ViewFig. 3-5. Advanced View submenus.Centering an ImageYou can center an image or images in a MatchSet/sc

PDQuest User Guide3-10Displaying Sections of an ImageTo display one of nine sections of an image or MatchSet/scanset, go the 3x3 Sections submenu on t

PDQuest User Guideviii

Viewing and Editing Images3-113.8 Density ToolsThe tools under the View>View Density submenu and on the Density Tools toolbar are designed for adva

PDQuest User Guide3-12Plot Density DistributionPlot Density Distribution displays a histogram of the signal intensity distribution for the entire imag

Viewing and Editing Images3-13Plot Vertical TracePlot Vertical Trace plots an intensity trace down a vertical line centered on the point where you cli

PDQuest User Guide3-14Fig. 3-9. List of Color Groups.Click a color group in the list to select it.Changing a ColorAfter you have selected the color g

Viewing and Editing Images3-15Saving/Selecting a Defined Set of ColorsAfter you have changed the colors within color groups, you can save these settin

PDQuest User Guide3-163.10 Multi-Channel ViewerYou can use the Multi-Channel Viewer to distinguish different types and levels of fluorescence in a gel

Viewing and Editing Images3-17Note: The color channel used to display an image in the viewer has no relation to the filter used when capturing the ima

PDQuest User Guide3-18Exporting and PrintingYou can export a 24-bit TIFF image of your merged view by clicking on the Export button. This will open a

Viewing and Editing Images3-19Fig. 3-13. 3D ViewerUse your mouse or keyboard to reposition and rotate the image.WindowsRotate the image - Left click

PDQuest User Guide3-20Zoom in/out - To zoom in or out, Click the center mouse button or roll the wheel. If you do not have a three button mouse or a m