Bio-Rad Quantity One User Guide
Quantity One
®
User Guide for Version 4.4
Windows and Macintosh
P/N 4000126-14 RevA
Quantity One User Guide
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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
3.6. Image Stack Tool .......................................................................................... 3-12
3.7. Colors ............................................................................................................ 3-14
3.8. Transform ...................................................................................................... 3-17
3.9. Resizing and Reorienting Images ................................................................. 3-23
3.10. Whole-Image Background Subtraction ....................................................... 3-29
3.11. Filtering Images .......................................................................................... 3-33
3.12. Invert Data ................................................................................................... 3-39
3.13. Text Overlays ................................... ............................................. ...... ........ 3-39
3.14. Erasing All Analysis from an Image ........................................................... 3-42
3.15. Sort and Recalculate .................................................................................... 3-42
3.16. Automation Manager .................................................................................. 3-42
4. Lanes .................................................................................. 4-1
4.1. Defining Lanes ................................................................................................ 4-1
4.2. Lane-Based Background Subtraction .............................................................. 4-9
4.3. Compare Lanes ............................................................................................. 4-13
4.4. Lane-based Arrays ........................................................................................ 4-16
5. Bands .................................................................................. 5-1
5.1. How Bands Are Identified and Quantified ..................................................... 5-2
5.2. Band Detection ................................................................................................ 5-3
5.3. Identifying and Editing Individual Bands ..................................................... 5-10
5.4. Plotting Traces of Bands ............................................................................... 5-12
5.5. Band Attributes ............................................................................................. 5-13
5.6. Band Information .......................................................................................... 5-16
5.7. Gauss-Modeling Bands ............................................................. .................... 5-18
5.8. Irregularly Shaped Bands in Lanes ............................................................... 5-21
6. Standards and Band Matching ...................................... ... 6-1
6.1. Standards ......................................................................................................... 6-1
6.2. Band Matching .............................................................................................. 6-13
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Contents
6.3. Quantity Standards ........................................................................................ 6-24
7. Volume Tools ..................................................................... 7-1
7.1. Creating a Volume .......................................................................................... 7-1
7.2. Moving, Copying, and Deleting Volumes ...................................................... 7-6
7.3. Volume Standards ........................................................................................... 7-7
7.4. Volume Background Subtraction ................................................................... 7-8
7.5. Volume Arrays .............................................................................................. 7-11
8. Colony Counting ................................................................ 8-1
8.1. Defining the Counting Region ........................................................................ 8-2
8.2. Counting the Colonies .................................................................................... 8-3
8.3. Displaying the Results .................................................................................... 8-4
8.4. Making and Erasing Individual Colonies ....................................................... 8-5
8.5. Using the Histogram to Distinguish Colonies ................................................ 8-6
8.6. Ignoring a Region of the Dish ........................................................................ 8-8
8.7. Saving/Resetting the Count ............................................................................ 8-9
8.8. Saving to a Spreadsheet ................................................................................ 8-10
9. Differential Display and VNTRs ........................................ 9-1
9.1. Differential Display ........................................................................................ 9-1
9.2. Variable Number Tandem Repeats ................................................................. 9-3
10. Reports ............................................................................. 10-1
10.1. Report Window ........................................................................................... 10-1
10.2. Lane and Match Reports ....................................................... ..... ................. 10-5
10.3. Band Types Report ..................................................................................... 10-6
10.4. 1-D Analysis Report ................................................................................... 10-8
10.5. Similarity Comparison Reports .................................................................. 10-9
10.6. Volume Analysis Report ........................................................................... 10-20
10.7. Volume Regression Curve ........................................................................ 10-23
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.
Gel Doc 2000 ............................................................................. A-1
Appendix B.
ChemiDoc .................................................................................. B-1
Appendix C.
ChemiDoc XRS ......................................................................... C-1
Appendix D.
GS-700 Imaging Densitometer ................................................ D-1
Appendix E.
GS-710 Imaging Densitometer ............................... .... ..... ..... ... E-1
Appendix F.
GS-800 Imaging Densitometer ................................................ F-1
Appendix G.
Fluor-S MultiImager ......................... ..... ..... ............................... G-1
Appendix H.
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.
VersaDoc ................................................................................... K-1
Appendix L.
Cross-Platform File Exchange ................................................ L-1
Appendix M.
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 W indow s and Macinto sh platforms. Any platform dif feren ces 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
File > Open Choosing the Open command under the File menu.
Dragging Positioning t he cursor on an object and hol ding down
the left mouse button while you move the mouse.
Ctrl+s Holding down the Control key while typing the letter s.
Right-click/
Left-click/
Double-click
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.
Clicking the right mouse button/
Clicking the left mouse button/
Clicking the left mouse button twice.
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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
1.1 Overview 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
1.2 Digital 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 ha s an X an d Y coo rdinate, an d a valu e Z. Th e X and Y c oordi nates
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 sy stem and
VersaDoc ™ imaging systems with white light illumination. Sig nal 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.
1.3 Gel 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
1.4 Quantity One Workflow
The following steps are involved in using Quantity One.
Acquire Image
Optimize Image
Lane and Band Analysis Volume Analysis Colony Counting
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.
1.5 Computer Requirements
This software is supporte d 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
Windows NT 4.0 with service pack 6
Windows 2000
Windows XP
Processor: Pentium ≥ 333 MHz
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Quantity One User Guide
RAM: ≥ 128 MB or better for Gel Doc, ChemiDoc, ChemiDoc
XRS, and VersaDoc systems.
≥ 256 MB or better for Molecular Imager FX systems,
Personal FX system, and GS-800 densitometer.
Hard disk space: ≥ 3 GB
Monitor: 17" monitor, 1024 x 768 resolution (absolutely required),
True color.
SCSI: Required for all Bio-Rad imaging devices except the Gel
Doc, ChemiDoc, ChemiDoc XRS, and VersaDoc systems.
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),
Millions of colors.
SCSI: Required for all Bio-Rad imaging devices except the Gel
Doc, ChemiDoc, ChemiDoc XRS, and VersaDoc systems.
Adaptec SCSI card recommended.
Printer: Optional.
Note: The default amount of memor y ass i gn ed to th is program on the Macintosh is 1 28
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
RAM. With the application icon selected, go to File > Get Info in your Finder to
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less than your total
Chapter 1. Introduction
reduce the memory requirements for the application. See your Macintosh
computer documentation for details.
1.6 Installation
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 d esktop and cre ate a fold er 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.
1.7 Hardware 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
1-8
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. Af ter yo u 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 incompatib le 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 mus t reboot th eir computer after in stalling t he HSK. W ind ows
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.
1.8 Starting the Program
The Hardware Security Key must be attached to the co mputer b efore yo u can st art 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 i c on.
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.
1.9 Software 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 th e
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 day s to p urchase the sof tware and obt ain a pu rchase o rder nu mber
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 Fo rm.
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-Ra d.
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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 , yo u can en ter the conten ts of the form into an e-mail and send it to BioRad at the address listed in the Registratio n 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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Quantity One User Guide
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 Inte rnet
You can download a trial version of the so ft wa re f rom Bi o- Rad’s Web s i te. Go to Th e
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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Chapter 1. Introduction
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 V ia 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 i ns talled and used simultaneously on unlimit ed
numbers of computers. Quantity One Basic is a limited version of the flexible and
powerful Quantity One.
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Quantity One User Guide
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 s ave images , h ow to set pref erences , an d 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 m enus that co ntain all the m ajor
features and functions available in the software.
• File—Opening and saving fi le s, imagi ng device contro ls, pri nti ng , exporti ng .
• 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 common ly used
commands. Next to the main toolbar are the status boxes, which provide information
about cursor selection and toolbar buttons.
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Quantity One User Guide
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 u seful Quick Guid es
(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
Preferences). You can also specify how long the Tool Help will remain displayed.
2.5,
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 expl anation about t hat command w ill be disp layed in thi s second statu s
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
Fig. 2-3. Secondary toolbar formats and features.
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
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.
2-3
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