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Quantity One®
User Guide for Version 4.4 Windows and Macintosh
P/N 4000126-14 RevA
Quantity One User Guide
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ii
Table of Contents
1. Introduction ........................................................................ |
1-1 |
1.1. Overview of Quantity One .............................................................................. |
1-1 |
1.2. Digital Data and Signal Intensity .................................................................... |
1-2 |
1.3. Gel Quality ...................................................................................................... |
1-3 |
1.4. Quantity One Workflow ................................................................................. |
1-4 |
1.5. Computer Requirements ................................................................................. |
1-5 |
1.6. Installation ...................................................................................................... |
1-7 |
1.7. Hardware Security Key (HSK) ....................................................................... |
1-8 |
1.8. Starting the Program ..................................................................................... |
1-10 |
1.9. Software License .......................................................................................... |
1-11 |
1.10. Downloading from the Internet .................................................................. |
1-14 |
1.11. Quantity One Basic ..................................................................................... |
1-15 |
1.12. Contacting Bio-Rad .................................................................................... |
1-16 |
2. General Operation .............................................................. |
2-1 |
2.1. Menus and Toolbars ....................................................................................... |
2-1 |
2.2. File Commands ............................................................................................... |
2-6 |
2.3. Imaging Device Acquisition Windows ......................................................... |
2-14 |
2.4. Exit ................................................................................................................ |
2-15 |
2.5. Preferences .................................................................................................... |
2-15 |
2.6. User Settings ................................................................................................. |
2-23 |
3 Viewing and Editing Images ............................................. |
3-1 |
3.1. Magnifying and Positioning Tools ................................................................. |
3-1 |
3.2. Density Tools .................................................................................................. |
3-5 |
3.3. Showing and Hiding Overlays ........................................................................ |
3-6 |
3.4. Multi-Channel Viewer .................................................................................... |
3-7 |
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Quantity One User Guide
|
3.5. 3D Viewer ..................................................................................................... |
3-10 |
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3.6. Image Stack Tool .......................................................................................... |
3-12 |
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3.7. Colors ............................................................................................................ |
3-14 |
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3.8. Transform ...................................................................................................... |
3-17 |
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3.9. Resizing and Reorienting Images ................................................................. |
3-23 |
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3.10. Whole-Image Background Subtraction ....................................................... |
3-29 |
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3.11. Filtering Images .......................................................................................... |
3-33 |
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3.12. Invert Data ................................................................................................... |
3-39 |
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3.13. Text Overlays .............................................................................................. |
3-39 |
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3.14. Erasing All Analysis from an Image ........................................................... |
3-42 |
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3.15. Sort and Recalculate .................................................................................... |
3-42 |
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3.16. Automation Manager .................................................................................. |
3-42 |
4. |
Lanes .................................................................................. |
4-1 |
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4.1. Defining Lanes ................................................................................................ |
4-1 |
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4.2. Lane-Based Background Subtraction .............................................................. |
4-9 |
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4.3. Compare Lanes ............................................................................................. |
4-13 |
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4.4. Lane-based Arrays ........................................................................................ |
4-16 |
5. |
Bands .................................................................................. |
5-1 |
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5.1. How Bands Are Identified and Quantified ..................................................... |
5-2 |
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5.2. Band Detection ................................................................................................ |
5-3 |
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5.3. Identifying and Editing Individual Bands ..................................................... |
5-10 |
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5.4. Plotting Traces of Bands ............................................................................... |
5-12 |
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5.5. Band Attributes ............................................................................................. |
5-13 |
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5.6. Band Information .......................................................................................... |
5-16 |
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5.7. Gauss-Modeling Bands ................................................................................. |
5-18 |
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5.8. Irregularly Shaped Bands in Lanes ............................................................... |
5-21 |
6. Standards and Band Matching ......................................... |
6-1 |
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6.1. Standards ......................................................................................................... |
6-1 |
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6.2. Band Matching .............................................................................................. |
6-13 |
iv
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Contents |
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6.3. Quantity Standards ........................................................................................ |
6-24 |
7. |
Volume Tools ..................................................................... |
7-1 |
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7.1. Creating a Volume .......................................................................................... |
7-1 |
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7.2. Moving, Copying, and Deleting Volumes ...................................................... |
7-6 |
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7.3. Volume Standards ........................................................................................... |
7-7 |
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7.4. Volume Background Subtraction ................................................................... |
7-8 |
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7.5. Volume Arrays .............................................................................................. |
7-11 |
8. |
Colony Counting ................................................................ |
8-1 |
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8.1. Defining the Counting Region ........................................................................ |
8-2 |
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8.2. Counting the Colonies .................................................................................... |
8-3 |
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8.3. Displaying the Results .................................................................................... |
8-4 |
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8.4. Making and Erasing Individual Colonies ....................................................... |
8-5 |
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8.5. Using the Histogram to Distinguish Colonies ................................................ |
8-6 |
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8.6. Ignoring a Region of the Dish ........................................................................ |
8-8 |
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8.7. Saving/Resetting the Count ............................................................................ |
8-9 |
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8.8. Saving to a Spreadsheet ................................................................................ |
8-10 |
9. Differential Display and VNTRs ........................................ |
9-1 |
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9.1. Differential Display ........................................................................................ |
9-1 |
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9.2. Variable Number Tandem Repeats ................................................................. |
9-3 |
10. Reports ............................................................................. |
10-1 |
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10.1. Report Window ........................................................................................... |
10-1 |
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10.2. Lane and Match Reports ............................................................................. |
10-5 |
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10.3. Band Types Report ..................................................................................... |
10-6 |
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10.4. 1-D Analysis Report ................................................................................... |
10-8 |
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10.5. Similarity Comparison Reports .................................................................. |
10-9 |
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10.6. Volume Analysis Report ........................................................................... |
10-20 |
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10.7. Volume Regression Curve ........................................................................ |
10-23 |
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10.8. VNTR Report ............................................................................................ |
10-25 |
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Quantity One User Guide
11. Printing and Exporting .................................................... |
11-1 |
11.1. Print Image and Print Actual Size ............................................................... |
11-1 |
11.2. Page Setup ................................................................................................... |
11-1 |
11.3. Image Report ............................................................................................... |
11-2 |
11.4. Video Print .................................................................................................. |
11-3 |
11.5. Export to TIFF Image ................................................................................. |
11-4 |
Appendix A. |
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Gel Doc 2000 ............................................................................. |
A-1 |
Appendix B. |
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ChemiDoc .................................................................................. |
B-1 |
Appendix C. |
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ChemiDoc XRS ......................................................................... |
C-1 |
Appendix D. |
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GS-700 Imaging Densitometer ................................................ |
D-1 |
Appendix E. |
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GS-710 Imaging Densitometer ................................................ |
E-1 |
Appendix F. |
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GS-800 Imaging Densitometer ................................................ |
F-1 |
Appendix G. |
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Fluor-S MultiImager .................................................................. |
G-1 |
Appendix H. |
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Fluor-S MAX MultiImager ......................................................... |
H-1 |
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Contents |
Appendix I. |
|
Personal Molecular Imager FX |
................................................. I-1 |
Appendix J.
Molecular Imager FX Family (FX Pro, FX Pro Plus and Molecular
FX) .............................................................................................. |
J-1 |
Appendix K. |
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VersaDoc ................................................................................... |
K-1 |
Appendix L. |
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Cross-Platform File Exchange ................................................ |
L-1 |
Appendix M. |
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Other Features ......................................................................... |
M-1 |
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Quantity One User Guide
viii
Preface
1. About This Document
This user guide is designed to be used as a reference in your everyday use of Quantity One® Software. It provides detailed information about the tools and commands of Quantity One for the Windows and Macintosh platforms. Any platform differences in procedures and commands are noted in the text.
This guide assumes that you have a working knowledge of your computer operating system and its conventions, including how to use a mouse and standard menus and commands, and how to open, save, and close files. For help with any of these techniques, see the documentation that came with your computer.
This guide uses certain text conventions to describe specific commands and functions.
Example |
Indicates |
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File > Open |
Choosing the Open command under the File menu. |
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Dragging |
Positioning the cursor on an object and holding down |
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the left mouse button while you move the mouse. |
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Ctrl+s |
Holding down the Control key while typing the letter s. |
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Right-click/ |
Clicking the right mouse button/ |
Left-click/ |
Clicking the left mouse button/ |
Double-click |
Clicking the left mouse button twice. |
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Some of the illustrations of menus and dialog boxes found in this manual are taken from the Windows version of the software, and some are taken from the Macintosh version. Both versions of a menu or dialog box will be shown only when there is a significant difference between the two.
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Quantity One User Guide
2. Bio-Rad Listens
The staff at Bio-Rad are receptive to your suggestions. Many of the new features and enhancements in this version of Quantity One are a direct result of conversations with our customers. Please let us know what you would like to see in the next version of Quantity One by faxing, calling, or e-mailing our Technical Services staff. You can also use Solobug (installed with Quantity One) to make software feature requests.
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1. Introduction
1.1Overview of Quantity One
Quantity One is a powerful, flexible software package for imaging and analyzing 1-D electrophoresis gels, dot blots, arrays, and colonies.
The software is supported on Windows and Macintosh operating systems and has a graphical interface with standard pull-down menus, toolbars, and keyboard commands.
Quantity One can image and analyze a wide variety of biological data, including radioactive, chemiluminescent, fluorescent, and color-stained samples acquired from densitometers, phosphor imagers, fluorescent imagers, and gel documentation systems.
An image of a sample is captured using the controls in the imaging device window and displayed on your computer monitor. Image processing and analysis operations are performed using commands from the menus and toolbars.
Images can be magnified, annotated, rotated, and resized. They can be printed using standard and video printers.
All data in the image can be quickly and accurately quantitated using the Volume tools.
The lane-based functions can be used to determine molecular weights, isoelectric points, VNTRs, presence/absence and up/down regulation of bands, and other values. The software can measure total and average quantities, determine relative and actual amounts of protein, and count colonies in a Petri dish.
The software can cope with distortions in the shape of lanes and bands. Lanes can be adjusted along their lengths to compensate for any curvature or smiling of gels.
Image files can be shared among all The Discovery Series™ software. Images can also be easily converted into TIFF format for compatibility with other Macintosh and Windows applications.
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Quantity One User Guide
1.2Digital Data and Signal Intensity
The Bio-Rad imaging devices supported by Quantity One are light and/or radiation detectors that convert signals from biological samples into digital data. Quantity One then displays the digital data on your computer screen, in the form of gray scale or color images.
A data object as displayed on the computer is composed of tiny individual screen pixels. Each pixel has an X and Y coordinate, and a value Z. The X and Y coordinates are the pixel’s horizontal and vertical positions on the image, and the Z value is the signal intensity of the pixel.
Signal intensity of a single pixel
Intensity |
3-D View
2-D View
Fig. 1-1. Representation of the pixels in two digitally imaged bands in a gel.
For a data object to be visible and quantifiable, the intensity of its clustered pixels must be higher than the intensity of the pixels that make up the background of the image. The total intensity of a data object is the sum of the intensities of all the pixels that make up the object. The mean intensity of a data object is the total intensity divided by the number of pixels in the object.
The units of signal intensity are Optical Density (O.D.) in the case of the GS-700™ imaging densitometer, GS-710™ calibrated imaging densitometer, and GS-800™ calibrated densitometer, the Gel Doc™ system, ChemiDoc™ system, ChemiDoc XRS™ system with a white light source, or the Fluor-S™ MultiImager system, Fluor-S™ MAX MultiImager system, Fluor-S™ MAX2 MultiImager system and VersaDoc™ imaging systems with white light illumination. Signal intensity is expressed in counts when using the Personal Molecular Imager™ system or the Molecular Imager FX™ system, Molecular Imager FX Pro™ fluorescent imager,
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Chapter 1. Introduction
Molecular Imager FX Pro Plus™ multiimager system, or in the case of the Gel Doc, ChemiDoc, ChemiDoc XRS, Fluor-S, Fluor-S MAX, or VersaDoc when using the UV light source.
1.3Gel Quality
Quantity One is very tolerant of an assortment of electrophoretic artifacts. Lanes do not have to be perfectly straight or parallel. Bands do not have to be perfectly resolved.
However, for accurate lane-based quantitation, bands should be reasonably flat and horizontal. Lane-based quantitation involves calculating the average intensity of pixels across the band width and integrating over the band height. For the automatic band finder to function optimally, bands should be well-resolved.
Dots that appear as halos, rings, or craters, or that are of unequal diameter, may be incorrectly quantified using the automatic functions.
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Quantity One User Guide
1.4Quantity One Workflow
The following steps are involved in using Quantity One.
Acquire Image
Optimize Image
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Lane and Band Analysis Volume Analysis |
Colony Counting |
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Report Results
Fig. 1-2. Quantity One workflow.
1.4.a Acquire Image
Before you can use Quantity One to analyze a biological image, you need to capture the image and save it as an image file. This may be done with one of the several BioRad imaging instruments supported by this software: the Molecular Imager FX and Personal Molecular Imager systems; the GS-700, GS-710, and GS-800 Imaging Densitometers; the Gel Doc, ChemiDoc, and ChemiDoc XRS gel documentation systems; the Fluor-S and Fluor-S MAX MultiImagers; and the VersaDoc.
The resulting images can be stored in files on a computer hard disk, network file server, or removable disks.
1.4.b Optimize Image
Once you have acquired an image of your sample, you may need to reduce noise or background density in the image. Quantity One has a variety of functions to minimize image background while maintaining data integrity.
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Chapter 1. Introduction
1.4.c Analyze Image
Once a “clean” image is available, you can use Quantity One to gather and analyze your biological data. In the case of 1-D gels, the software has tools for identifying lanes and defining, quantifying, and calculating the values of bands. Volume tools allow you to easily measure and compare the quantities of bands, spots, or arrays. The colony counting controls allow you to count the number of colonies in a Petri dish, as well as perform batch analysis.
Qualitative and quantitative data can be displayed in tabular and graphical formats.
1.4.d Report Results
When your analysis is complete, you can print your results in the form of simple images, images with overlays, reports, tables, and graphs. You can export your images and data to other applications for further analysis.
1.5Computer Requirements
This software is supported on Windows 98, XP, NT 4.0, and 2000, or on a Macintosh PowerPC.
The computer memory requirements are mainly determined by the file size of the images you will scan and analyze. High-resolution image files can be very large. For this reason, we recommend that you archive images on a network file server or highcapacity removable disk.
PC
The following is the recommended system configuration for installing and running on a PC:
Operating system: |
Windows 98 SE |
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Windows NT 4.0 with service pack 6 |
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Windows 2000 |
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Windows XP |
Processor: |
Pentium ≥ 333 MHz |
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Quantity One User Guide
RAM: |
≥ 128 MB or better for Gel Doc, ChemiDoc, ChemiDoc |
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XRS, and VersaDoc systems. |
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≥ 256 MB or better for Molecular Imager FX systems, |
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Personal FX system, and GS-800 densitometer. |
Hard disk space: |
≥ 3 GB |
Monitor: |
17" monitor, 1024 x 768 resolution (absolutely required), |
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True color. |
SCSI: |
Required for all Bio-Rad imaging devices except the Gel |
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Doc, ChemiDoc, ChemiDoc XRS, and VersaDoc systems. |
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Adaptec SCSI card recommended. |
Printer: |
Optional. |
Macintosh
The following is the recommended system configuration for installing and running on a Macintosh:
Operating system: |
System 9.0 or higher, excluding Mac OS X. |
Processor/Model: |
PowerPC G3 processor or better. |
RAM: |
≥ 256 MB for all Bio-Rad imaging systems. |
Hard disk space: |
≥ 3 GB |
Monitor: |
17" monitor, 1024 x 768 resolution (absolutely required), |
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Millions of colors. |
SCSI: |
Required for all Bio-Rad imaging devices except the Gel |
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Doc, ChemiDoc, ChemiDoc XRS, and VersaDoc systems. |
|
Adaptec SCSI card recommended. |
Printer: |
Optional. |
Note: The default amount of memory assigned to this program on the Macintosh is 128 MB. If the total RAM in your Macintosh is 128 MB or less, you should reduce the amount of memory assigned to the program to 10 MB less than your total RAM. With the application icon selected, go to File > Get Info in your Finder to
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Chapter 1. Introduction
reduce the memory requirements for the application. See your Macintosh computer documentation for details.
1.6Installation
1.6.a Windows
Note: Windows NT and 2000 users: You must be a member of the Administrators group to install The Discovery Series software. After installation, members of the Users group must have “write” access to The Discovery Series folder to use the software.
Insert The Discovery Series CD-ROM into your computer. The installer will start automatically. (If the CD does not auto-start, use Windows Explorer to open the root directory on the CD-ROM and double-click on the Setup.exe file.)
The installer program will guide you through the installation. The installer will create a default directory under Program Files on your computer called Bio-Rad\The Discovery Series (you can select your own directory if you wish). The application program will be placed in the Bin folder inside The Discovery Series folder. Additional directories for storing user profiles and sample images will also be created
The installer will place an application icon on your desktop and create a folder named The Discovery Series under Programs on your Windows Start menu.
After installation, you must reboot your computer before using an imaging device.
1.6.b Macintosh
Insert The Discovery Series CD-ROM into your Macintosh. The TDS-Mac folder will open on your desktop, displaying the installers for The Discovery Series applications. Double-click on the installer for your application.
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Quantity One User Guide
Fig. 1-3. Installation program icon (Macintosh).
The installer will guide you through a series of screens. The installer will create a folder on your hard drive that contains the main application and associated sample images (you can select a different folder if you wish). The installation will also create a folder called The Discovery Series in the Preferences folder in your System folder; this contains the Help file and various system files.
Once installation is complete, the folder containing the application icon will appear open on your desktop.
1.7Hardware Security Key (HSK)
Note: Initial installation of a network server does require the Hardware Security Key included in the software package. Installation of an additional Network Client User to a Network License Server System does not require an HSK. Please refer to the Network License Installation Guide that ships with Network Licenses.
The Discovery Series software is password-protected using a Hardware Security Key (HSK), which is included in your software package. You must attach the Hardware Security Key to your computer before you can run the software.
1.7.a Windows
Fig. 1-4. PC Hardware Security Key
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Chapter 1. Introduction
Before proceeding, please turn off your computer.
The HSK attaches to the parallel port on the back of your PC. If a printer cable is attached to this port, turn off the printer and disconnect it. After you have attached the HSK, you can attach the printer cable to the key itself and restart your computer and printer.
Note: Some parallel port devices such as zip drives may be incompatible with HSKs. Please check with your peripherals vendor.
The code for the PC hardware security key is EYYCY. This is printed on the key itself.
You will also need to install the system driver that allows the computer to recognize the HSK.
Note: Windows NT and 2000 users must be in the local administrator group to install the HSK driver.
To install the driver, open the Windows Start menu and select Programs > The Discovery Series. Select Install HASP Hardware Security Key Driver to begin installation.
Note: Windows 98 users must reboot their computer after installing the HSK. Windows XP, NT and 2000 users do not have to reboot.
1.7.b Macintosh
Fig. 1-5. Macintosh Hardware Security Key
Before proceeding, please turn off your Macintosh.
The Macintosh HSK must be inserted in the Apple Desktop Bus (ADB) path. The ADB port is located on the back of your Macintosh.
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Quantity One User Guide
Fig. 1-6. Apple Desktop Bus icon on back of Macintosh.
The HSK can be inserted at any point in the ADB path—between the computer and the keyboard, between the keyboard and the mouse, between the keyboard and the monitor, etc. After you have attached the HSK, you can restart your computer.
The code for the Macintosh HSK is QCDIY. This code is printed on the key itself.
Note: If your Macintosh does not have an ADB, you may use an ADB-USB converter.
1.8Starting the Program
The Hardware Security Key must be attached to the computer before you can start the software (unless you are using a network license).
1.8.a Windows
The installation program creates an application icon on your desktop. To start the program, double-click on this icon.
Fig. 1-7. Application icon.
You can also start the program from the Windows Start menu. Click on the Start button, select Programs, select The Discovery Series, and select the application name.
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Chapter 1. Introduction
1.8.b Macintosh
After installation, the main application folder will be open on your desktop. To start the program, double-click on the application icon shortcut inside the folder. You can move this shortcut icon to your desktop.
1.9Software License
When the software opens for the first time, you will see a Software License screen that shows the current status of your software license.
With a new HSK or network license, you receive a 30-day temporary license (“Your license will expire on _______”). The temporary license is designed to give you time to purchase the software, if you have not already done so.
Fig. 1-8. Temporary license screen.
During the 30-day period, the Software License screen will appear every time you open the software. To use the software during this period, click on the Run button.
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Quantity One User Guide
Network license holders can click on the Check License button at any time during the 30-day period to activate their full network license. (If your network license is not activated when you click on Check License, notify your network administrator.)
HSK users have 30 days to purchase the software and obtain a purchase order number and software serial number from Bio-Rad. When you have this information, click on the Check License or Registration Form button in the Software License screen to register your software.
Fig. 1-9. Software License Registration Form.
Fill out the information in the Software License Registration Form. Be sure to enter your purchase order number and software serial number under the Purchase Information tab when registering.
1.9.a Registering by Internet
If you have Internet access from your computer, click on the Submit via Internet button to send the Software Registration Form directly to Bio-Rad.
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Chapter 1. Introduction
Your information will be submitted, and a temporary password will be generated automatically and sent back to your computer. Simply continue to run the application as before.
Bio-Rad will confirm your purchase information and generate a permanent license. After 2–3 days, click on Check License in the Software License screen again to update to a permanent password. (The Software License screen will not appear automatically after the temporary password has been generated; the software will simply open normally. Go to the Help menu and select Register to open the Software License screen.)
1.9.b Registering by Fax or E-mail
If you do not have Internet access, click on the Print button in the Software License Registration Form and fax the form to Bio-Rad at the number listed on the form. Alternatively, you can enter the contents of the form into an e-mail and send it to BioRad at the address listed in the Registration Form.
Bio-Rad will contact you by fax or e-mail in 2–3 days with a full license.
1.9.c Entering a Password
If you fax or e-mail your registration information, you will receive a password from Bio-Rad. You must enter this password manually.
To enter your password, click on Enter Password in the Software License screen. If you are not currently in the Software License screen, select Register from the Help menu.
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Fig. 1-10. Enter Password screen.
In the Enter Password screen, type in your password in the field.
Once you have typed in the correct password, the OK light next to the password field will change to green and the Enter button will activate. Click on Enter to run the program.
1.10 Downloading from the Internet
You can download a trial version of the software from Bio-Rad’s Web site. Go to The Discovery Series download page at www.bio-rad.com/softwaredownloads and select from the list of applications. Follow the instructions to download the installer onto your computer, then run the installer.
After installation, double-click on the application icon to run the program. The software will open and the Software License screen will be displayed.
Note: If you attempt to start the downloaded program and receive an “Unable to obtain authorization” message, you will need a Hardware Security Key to run the program. Contact Bio-Rad to obtain a key.
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Fig. 1-11. Free Trial screen.
In the Software License screen, click on the Free Trial button. This will open the Software License Registration Form. Enter the required information (you will not have a purchase order number or software serial number, and can leave these fields blank) and click on Submit Via Internet.
A free trial password will be automatically downloaded to your computer. This password will allow you to use the software for 30 days.
If you decide to purchase the software during that period, contact Bio-Rad to receive a software package and a Hardware Security Key. You can then complete the registration process as described in the previous sections.
1.11 Quantity One Basic
Quantity One can be run in Basic mode. Quantity One Basic does not require a software license. The program can be installed and used simultaneously on unlimited numbers of computers. Quantity One Basic is a limited version of the flexible and powerful Quantity One.
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The following functionality is active in Basic Mode: Image acquisition with Bio-Rad imaging devices, Transform, Crop, Flip, Rotate, Text Tool, Volume Rectangle Tool, Volume Circle Tool, Density Tools, Print, Export to TIFF, and Save.
1.12 Contacting Bio-Rad
Bio-Rad technical service hours are from 8:00 a.m. to 4:00 p.m., Pacific Standard Time in the U.S.
Phone: 800-424-6723
510-741-2612
Fax: 510-741-5802
E-mail: LSG.TechServ.US@Bio-Rad.com
For software registration:
Phone: |
800-424-6723 (in the U.S.) |
|
+1-510-741-6996 (outside the U.S.) |
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2. General Operation
This chapter describes the graphical interface of Quantity One, how to access the various commands, how to open and save images, how to set preferences, and how to perform other basic file commands.
2.1 Menus and Toolbars
2.1.a Menu Bar
Quantity One has a standard menu bar with pulldown menus that contain all the major features and functions available in the software.
•File—Opening and saving files, imaging device controls, printing, exporting.
•Edit—Preferences, other settings.
•View—Image magnification and viewing tools, tools for viewing image data.
•Image—Image transform, advanced crop, image processing and modification.
•Lane—Lane-finding tools.
•Band—Band-finding and band-modeling tools.
•Match—Tools for calculating molecular weights and other values from standards, tools for comparing lanes and bands in lanes.
•Volume—Band quantity and array data tools.
•Analysis—Colony counting, Differential Display, VNTR analysis.
•Reports—Band and lane analysis reports, Phylogenetic Tree, Similarity Matrix.
•Window—Commands for arranging multiple image windows.
•Help—Quick Guides, on-line Help, software registration.
Below the menu bar is the main toolbar, containing some of the most commonly used commands. Next to the main toolbar are the status boxes, which provide information about cursor selection and toolbar buttons.
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2.1.b Main Toolbar
The main toolbar appears below the menu. It includes buttons for the main file commands (Open, Save, Print) and essential viewing tools (Zoom Box, Grab, etc.), as well as buttons that open the secondary toolbars and the most useful Quick Guides (Printing, Volumes, Molecular Weight, and Colony Counting).
File commands |
Viewing commands |
Toolbars |
Quick Guides |
Fig. 2-1. Main toolbar.
Tool Help
If you hold the cursor over a toolbar icon, the name of the command will pop up below the icon. This utility is called Tool Help. Tool Help appears on a time delay basis that can be specified in the Preferences dialog box (see section 2.5, Preferences). You can also specify how long the Tool Help will remain displayed.
2.1.c Status Boxes
There are two status boxes, which appear to the right of the main toolbar.
Fig. 2-2. Status boxes.
The first box displays any function that is assigned to the mouse. If you select a command such as Zoom Box, the name and icon of that command will appear in this status box and remain there until another mouse function is selected or the mouse is deassigned.
The second status box is designed to supplement Tool Help (see above). It provides additional information about the toolbar buttons. If you hold your cursor over a
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Chapter 2. General Information
button, a short explanation about that command will be displayed in this second status box.
2.1.d Secondary Toolbars
Secondary toolbars contain groups of related functions. You can open these toolbars from the main toolbar or from the View > Toolbars submenu.
The secondary toolbars can be toggled between vertical, horizontal, and expanded formats by clicking on the resize button on the toolbar itself.
Expanded format |
Horizontal format |
Vertical format |
Hold cursor over icon to reveal the “tool tip”
Click on question marks for on-line help
Click on resize button to toggle format
Fig. 2-3. Secondary toolbar formats and features.
The expanded toolbar format shows the name of each of the commands. Click on the ? icon next to the name to display on-line Help for that command.
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