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The original Cytometry software catalog was developed and managed by Dr. Eric Martz for several years. In cooperation with Dr. Martz, the site will now be managed by the Purdue University Cytometry Laboratories.
Our goal is to provide comprehensive educational materials in all areas of cytometry and broadly in science where we can. If you want to contact Dr.
Martz please do so. This catalog strives to be comprehensive — to include as much free flow cytometry software as possible. We have also added some demonstrations of commercial packages. Report comments, catalog omissions and corrections to jpr flowcyt. Problems getting program files? Here’s HELP. Cytospec is useful for hyperspectral analysis and is a really easy program to use and does PCA as well on regular listmode files.
PlateAnalyzer handles lots of big data sets – any number of parameters – can handle CyTOF data no problems, does high throughput screening using 96, well plates nicely.
Does dose response curves, and has a great number of advanced features. Free Software is Here. This is a set of tools based on open code with “R” – you need to be a bit advanced to use these tools.
Here is the link. A decent package whcih you can download from here. FlowCytometryTools is a python package for visualization and analysis of high-throughput flow cytometry data. Best available for general purposes; colored regions, quadrant analysis, complex gating. Gorgeous graphics, 3D contour and dot plots. Version 2. If you need to run under Soft Windows on a Macintosh , get the special version that uses the instruction set. Jump back to contents.
Back to software index. Fast batch analysis of listmode files including graphics and overlays, fully corrected intensities, automatic peak detection, kinetics, calculated parameters, gate ratios. Spreadsheet-ready medians. Tutorial with sample data. Does not do quadrant analysis. Works perfectly in Windows.
Full documentation and the program are available from the MFI Home page. Information about the included program Included source code Included data files. General purpose program with many graph formats to facilitate the comprehension of multi-parameter data. Also provides cell cycle analysis , neural net clustering, batch mode support, composite graph generation from multiple files , up to 10 rectangular or irregular regions of interest for color highlighting between parameters or editing, and several forms of hardcopy output PS, HPGL, PCL, GIF, PICT.
Powerful and flexible general purpose data analysis and manipulation interpreter which uses FCS-type storage format. Does histogram overlays, 2D and 3D contour plots. Scripts exist for flow data which can be reprogrammed as needed.
General purpose with polygonal gates mouse controlled , contour and density plots, histogram overlays, kinetics vs. New parameters can be created by transformation and division. Supports only one printer, the HP Paintjet. Comp Biomed Res , WinMDI has more flexible gating logic, better numeric results for histograms and marked segments of histograms, better control of color or line type for overlayed histograms. EXE by ftp. This is an old but elegant scatter gating and quadrant analysis program provided to the public domain by Becton-Dickinson.
It determines percentage positive cells from FCS1. After you have set the gate typically on FSC vs. SSC or scatter vs. However, it displays the dot plot and histograms for each file for a user-specified number of seconds during which pressing any key allows modifications.
Simple-minded but actually quite slick. C source code is included. This verification suite provides tools for generating FCS Flow Cytometry Standard format data files with known contents.
It is provided as a companion to MFI but is suitable for verification of any program capable of reading generic FCS files. Tests with synthetic data represent one of several methods of verifying accuracy of results. However, the programs can be used under DOS to generate additional data files which can then be moved to any operating system. The suite includes the program A2FCS. It can handle 8- or bit data, and can mark the data as log-acquired.
Programs are provided to generate columns of random numbers; the results medians etc. The programs can generate arbitrarily large FCS files of repeating cycles of random numbers hence with known medians, etc. MFI has been tested using this strategy for up to 2,, events of 3 parameters each. Tools are also provided for generating data to display the greeting of your choice as a dot plot. This utility permits test data generated mathematically to be used to test flow analysis software.
Note: an alternative implementation, A2FCS. It may be started automatically or manually after the computer has booted. Users will be required to “log-in” with their initials and a password. An optional “welcome” or “news” screen is displayed at login. Log-in and log-out dates and times for each user are recorded in a data file, which may be searched and printed by date and the users’ “group” assignment such as lab affiliation or billing account number.
This data may also be saved in a file suitable for import in spreadsheet or database programs. Only “System Administrators” may enter and remove users or make changes to the system-use log file.
TXT , containing detailed instructions on how to do this. It is designed to generate a list of scatterplot points to be read by some other analysis, statistics, or graphics program. GENP documentation. It is used when it is convenient to have histogram data in a human readable format, or when the data needs to be read by a standard analysis or statistics program.
Authors: J. Another utility program reverses the byte order of the binary listmode data in FCS1. A macintosh utility to convert FCS1. It also adds calculated ratio, and time parameters and saves in FCS2. The program outputs three types of text file: raw list mode data, histogram data, and line graph data eg mean Calcium v Time. It can handle up to 16 parameters, and allows the user to delete redundant parameters to make space.
At present only Mac format FCS2. Editor’s note: MFI , a DOS package, also calculates and normalizes the ratio of two existing parameters, and plots any parameter vs.
See also Refresh Ratio. Source Code: “Too Embarrassing to Distribute”. Author: Ray Hicks rh cus. Prints cytometer settings as recorded in files acquired with CellQuest tm Becton-Dickinson version 1. Provided without warranty by its author, Ted Kunich, TedKunich value. Normalizes flow cytometric immunophenotyping data to a biological standard.
This program is under development. It is untested on other FCS2. Compatible with linear or log data, or channel resolution. Report problems or incompatibilities to him. The program was written in Visual Basic 3. Source code is not provided. Catalog editor’s note: MFI see elsewhere in this catalog can calculate the ratio of two user-specified parameters, and rescale the result in several optional ways. Unlike Refresh Ratio, MFI calculates the ratio during analysis, and does not write it to the listmode file.
Get Refresh Ratio , or visit their home page. This is a pair of programs which transfer files, including listmode files, between Hewlett-Packard HP Pascal 3. Transfer can occur in either direction. Transfer takes about 30 seconds per 10, event listmode file.