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- Local and Global Preferences
- Gate/Region Names
- 'Slow'and 'Quick' Statistics
- Saving Run Routine Results
- Unique Features of FCAP-list
- Color Compensation
- Principles of Smart Gates
- Batch Processing
- Differences Between the Routine and the Project?
- Versions for IBM PC
- What are the program variables good for?
- Report Generation
- Discount for Research Laboratories and Educational Institutions
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In FCAP-list, you can define the following Preferences:
The global preferences are saved when you quit FCAP-list. Certain preferences, including byte order, parameter names, routine saving options and statistics, can be chanched locally. Local setting is valid until you quit FCAP-list.
The preferences are described in Chapter 1 of the FCAP-list User's Guide.
Copying and pasting gates from one plot to another may result in two gates having the same name on the same histogram or bivariate distribution plot. Because FCAP-list identifies each gate according to its name, the Gate Manager of FCAP-list will find only one of the gates that have the same name. In order to avoid the error that is due to the name conflict, one of the involved gates must be renamed before the next Classify command is executed, or the statistical results are calculated.
Internally, FCAP-list uses two algorithms to determine the number and percentage of events in distributions and in gates/regions: A quick statistics and a slower one. The calculation of the 'quick' algorithm is based on the use of the frequency distributions. The distributions are are saved in 256 channel single parameter distributions and in a 64x64 matrix. The slower algorithm uses the original listmode data as input values, which represents a better precision than the distribution-based approximation. The results of the 'quick statistics' appear in the Statistics window. On the other hand, the results that are saved into the Report or Page document are determined directly from the listmode data file.The two results may, therefore, slightly differ from each other.
The saving options of the Run Routine batch processing are different from the general saving options set in the New... or Open... commands from the File menu. As a default location, the Report, Page and Spreadsheet commaands are saved into that folder from which the first data file is taken. The default saving options are specified in the Routine Results preferences.
FCAP-list is a population oriented data analysis software. The 'populations', like lymphocytes, CD8+ T cells, granulocytes, etc. are classified by a set of linear and polygon gates.
FCAP-list has a gate fine-tuning algorithm for automatic data analysis on a series of slightly different samples. The so-called 'Smart Gates' are able to offset their position and 'find' a population which shifted due to instrument drift and differences in cell staining procedure, etc.
FCAP-list provides two gating procedures:
The time-gating, i.e. the kinetic versus time data analysis, is an additional gating option which can be applied with the above gating procedures in any combination.
Populations are selected by parallel gating in which the gates are defined with independent gate-defining (drawing) steps. A population is determined by all gates of the same color.
You can activate hierarchical gating if you double click within a previously drawn gate or region. FCAP-list creates a new frequency distribution - histogram or dot plot - from the events which are within the double clicked gate. You can draw gates/regions on the new distribution and define additional descendant populations by double clicking on these gates. You can continue this protocol and build a complex system of hierarchical gates and a tree of corresponding distribution hierarchy.
Batch Analysis:
The unique gating method of FCAP-list allows to build sophisticated data analysis protocols. Any protocol can be saved into a routine document for batch analysis of samples that have been stained with the same method. In addition, one can save batch processes and complex data handling algorithms as computer programs (projects) written in the high level programming language called FCAP BASIC. The interpreter of the language is inherent part of FCAP-list.
In summary, no other flow cytomtry data analysis software provides as wide line of data analysis tools as FCAP-list. Many of the tools, like Smart Gates, the advanced graphics tools, the built in high level programming language, the innovative algorithm for auto fluorescence correction on cell-by-cell basis, etc., are not available in any other computer software.
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The color compensation algorithm is based on mathematical subtraction os a fraction of one signal from another. The method allows you to correct simultaneously the spillover of any number of fluorochromes.
FCAP-list allows you to perform color compensation in three ways:
1. Without autofluorescence correction.
2. With cell-by-cell autofluorscence correction.
3. With autofluorescence correction by subtracting average autofluorescence
of a control sample.
Prior to applying color compensation, you should measure specific test samples with the very same instrument setting that is used for acquiring the experimental samples.
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The smart gates are able to offset their position to correct day-to-day or experiment-to-experiment shifts in populations that can occur due to instrumental drift, differences in sample preparation conditions, etc. In smart gates, you associate 'smart gate centers' to a set of linear gates and/or polygon gates. The use of smart gates eliminates the need for manual gate adjustment in the batch analysis processes.
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FCAP-list allows you to save data analysis algorithms in two document types:
Routines Projects Differences Between the Routine and the Project
A routine saves a data analysis protocol in binary format. A routine is a static object, i.e. it generates a set of output and results from one single 'input' listmode data file in one classification step.
A project, on the other hand, saves data in ASCII text. The data analysis steps are coded with statements, commands and functions of a high level programming language called FCAP BASIC. A project is a sequence of analysis steps. Unlike a routine, a project can handle several listmode data files, transfer result(s) from one process to another, etc. In FCAP-list, the projects are executed with the built-in FCAP BASIC interpreter.
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The FCB software allows you to run Project documents in DOS environment. FCB is essentially an FCAP BASIC interpreter.
The release of the 32 bit Windows version of FCAP-list will be announced this year.
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Variables allow you to pass numerical values from one routine or project to another, or from one execution of FCAP-list to the next.
For example, one can save the mean autofluorescence intensity determined on unstained sample into the variable called 'afl1', and perform a simple autofluorescence correction by subtracting 'afl1' from the data acquired on stained samples.
Variables may be used to save parameters of calibration curves, standards, etc.
Variables are named values. A typical variable name contains letters and numbers. A variable name can be any character set which is a legal variable name in FCAP BASIC.
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FCAP-list v1.20 provides several saving options:
Report file: Saves statistical results into a text document, including your comments and explanations Graphic Page Output: Saves PICT documents of histograms, dot plots, etc., organized in printable page format. The major quadrant and region statistics appear on the graphs Spreadsheet: Saves statistical results, distribution data and listmode data in spreadsheet format for use with third party applications (MS Excel, Claris Works, StatWiev, etc.) Listmode and distribution (histogram, dot plot) data in FCS2.0 format Graphics created with the built-in drawing tools of FCAP-list (PICT) Utility files: Routine documents, project documents, region and gate settings, program variables, color compensation matrix, etc.
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Yes, we provide FCAP-list for a special price for universities and university research labs.
For more information,
contact us by e-mail: softfow@wavefront.com send a fax message to (612)-895-0900 (USA) or +36-72-24-00-64 (Hungary) call 1-800-956-0100 (USA) or +36-72-24-00-64 (Hungary)
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