The FCSExtract application was developed to be a small utility that will allow you to extract Flow Cytometry Standard (FCS) data from a binary FCS file and convert it to an ASCII text format, which can be read by a variety of software analysis packages. An example of working with this data in R is provided.
You may be frustrated if you attempt to analyze your flow cytometery data in a FCS file using any third-party software analysis tool. The FCS file is a binary file, and contains a number of non-ASCII text characters, which are unprintable, and unreadable by many programs. You cannot just load a FCS file into Excel or other analysis tool easily.
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The FCSExtract application was developed to extract data from a FCS binary file and convert it to a form suitable for software analysis packages.
You may have been reading or writing Excel files, or some other type of spreadsheet, and wondered if you could import or export the FCS data stored in the file for use in analysis packages. Sometimes the software you would like to use does not recognize the data in the FCS file.
Alternatively, you might be working with other analysis tools that do not have the capability to analyze the data stored in a FCS file.
FCS Extract Features:
The application is configured to allow the selection of a file to open from the file system. You can specify what type of file to open. The application allows you to either import the file or export the data to a text file for analysis.
The data can be imported directly to an analysis program such as Excel, R, IPET, UNIX text editors, etc. The data can also be exported to a file that can be used by software tools such as Microsoft Outlook, Rexx, etc.
The FCS data can be exported in either binary or ASCII format. There is no requirement to specify a particular data file format.
The data is represented in both binary and text format. This allows the file to be «read» by a variety of different software packages that can interpret the data in a variety of formats, such as.txt,.csv, or.csv.
FlowCore Flow Cytometry:
FCSExtract is written to be compatible with the FlowCore Flow Cytometry data format. A FlowCore-compatible library is included. The FlowCore command-line tools can be used to read data in FCS format. You can also use the FlowCore-compatible library to convert FlowCore binary files into FCS format. This library has been developed into the FlowCore Data Abstraction Layer (DAL), which can be used to convert data between FCS format, ArcGIS, Excel, iWorks, or whatever you may require.
Version 1.0.0.00 was released on August 16, 2012.
Version 1.2.0.00 was released on April 17, 2013.
Version 1.3.0.00 was released on November 19, 2013.
Version 1.4.0.00 was released
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The FCSExtract Application is a small desktop utility that will be able to extract FCS files from a variety of vendors and format them in an ASCII (text) format.
FCSExtract has a GUI (graphical user interface) that allows you to select the source and destination files, browse and extract FCS files from your hard disk, preview the source FCS files in a folder tree in either Binary or ASCII format and export your selections into a chosen ASCII format to save space on your hard disk.
The GUI allows you to choose the working file formats, including FTP, SFTP, HTTP and FCP, to download files from a server. The script uses FTP when downloading files from a local server, and SFTP when downloading files from a server on the Internet.
The GUI allows you to use either the FCS (Binary) or FCS-Ascii (ASCII) file extension to rename file extensions to your liking. It is a good idea to use the FCS-Ascii extension to convert your data to ASCII format.
Although the FCSExtract GUI works in the Terminal, it is recommended that you run the program from a Microsoft Windows (such as Windows 8) desktop environment.
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FCSExtract (Program) was developed for use with Windows 7. It reads binary data from an FCS file and converts it into a text file. The ASCII text file can be read by many software analysis tools that work with text files. The original file is left as a backup in the same directory as the text file. The original binary file can be loaded into CellQuest or FlowJo again to view the original data.
FCS Extract has been created primarily for students and researchers, and users that do not want to have to deal with the headaches that come from trying to read a FCS file.
FCSExtract will read and save FCS files with the following file extensions:
(if you are not sure of the file type you can load the file into a program and look for the appropriate file type in the menu to find the correct type)
*(A windows limitation, although it is unclear if this is the default file extension for a FCS file)
**Before running the software, it is advisable to back-up the original file as a.txt file in the same directory as the.fcs file.
Loading of files into FCS Extract:
All files can be loaded using the Open/Load buttons. In addition, all text files in a directory can be selected and loaded at once if no buttons are pressed while selecting the file.
This utility will search the file system for the FCS file or files in a directory of your choice. The user must specify the full path to the FCS file(s) that they want to extract from.
Version 2.2 – [04/08/2013] – Correction on handling multiple FCS files with the same name in the directory. New progress bar added.
Version 2.1 – [03/30/2013] – Fixed file name error that was reported with older versions of the utility.
Version 2.0 – [03/26/2013] – New FCS file format introduced. This version makes use of the new FCS format introduced by Thermo Fisher Scientific. Download Version 1.0 for information on this new format
Version 1.0 – [03/24/2013] – Started from scratch with completely different format.
In addition to creating a text file, the original binary file is backed up in the same
What’s New in the FCS Extract?
FCSExtract allows you to import and export flow cytometric datasets in different FCS-ASCII file formats (with example FCS files included). You can also save out the original FCS file using its own algorithm for converting any FCS text to ASCII, which can then be converted into the designated file type by any ASCII text editor.
FCSExtract Version 2.0 (TAMU):
Since version 2.0:
Ability to extract a whole group from a txt file
Multi-user and multi-computer saves/loads
Import FCS (Binary) file to ASCII format with all associated metadata
Import FCS files into text files with a custom formatter
Extract all metadata text from FCS file into the text file
Export FCS (ASCII) file with all associated metadata as a text file
Write FCS (ASCII) file in the designated name with the specified formatter
Convert any FCS text to ASCII
Example 1: Example of Worked Data:
Example 2: Save to Txt:
Example 3: Save to CSV:
Example 4: Save to CSV with Multi-User Support:
Installation on Linux or Windows:
FCSExtract is a stand-alone application and does not require any other application or driver on your computer. You can download and run this application from the following two sites:
FCSExtract is available from a stand-alone executable file that is ready to use on most platforms. To install this application, download the «FCSExtract» file from the above web site and unzip it in a directory of your choice.
Double-click on the «fcsextract.bat» file to begin installation. The software will install and create a directory to the operating system. If you are installing this application for the first time, a window will open where you must input your installation directory. Once you have indicated your desired directory, the software will copy the executable files in the directory to that location.
If you wish to change the installation location, you can
To install and run DLC Pack 1 you need:
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7 GB free hard drive space
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Installing DLC Pack 1 will overwrite some of your saved files, so make sure you have a back-up of all your files and your saves.
To install DLC Pack 2 or DLC Pack 3 you need: