MyCyte

MIFlowCyt, the minimum information required for reporting a flow cytometric experiment, was accepted in March of this year by ISAC as the standard detailing what information the Analytical Cytometry Standard (ACS) should contain, but specifies nothing regarding the format of the newest data file standard (Unfamiliar with the ACS?  View my previous post here ). The discussion within our community has now turned to what that format will be.  At the ISAC meeting in Budapest, the Data Standards Task Force (DSTF) hosted several discussions and assembled the attending members for a meeting in an attempt to gauge the prevailing opinions on what the format needs to be for ACS.  The conclusion was that the ACS file itself should be a container file, meaning that it stores a number of other data containing files that can be of a variety of formats.  The task force agreed that this was the best way to capture a large amount of metadata while recording the actual measurements in a format that could lack most header information and thus be read by a wide array of non-proprietary software.

If the ACS file is a container, what types of files should it hold?  There was little debate that one of the files should be an index.  There must be a second file type that would contain the actual measurements, and then additional files to contain the metadata.  The meeting at ISAC began with a debate on the type of container to use.  A Zip file was presented as the most viable option with some dissenting.  Next the standard for storing the measurements was debated and the Network Common Data Form, abbreviated as netCDF, will be the preferred form, though FCS can still be used.  NetCDF is an open source binary-like file format that has been used in many scientific fields for data storage.  As for the metadata, the task force was in agreement that some kind of text document needed to be produced to contain the information on what type of cytometer was used to collect the data, what was the configuration and settings on the machine, what was the compensation, and what gates were created to produce the analytical results.  The task force has thus far proposed a series of XML files to contain this information.  Gating-XML and Instrumentation-ML are two proposals to contain this information.  The format of the container allow for the possibility of including other files, such as files that include the experimental description, analysis results, or whatever else one would like to include in their documentation.
This is a topic that will concern most flow users, and the task force realizes that they are just a sampling of the total usership.  The more users that we can hear the opinions of, the better the standard will reflect what the users want, so the conclusions of the task force have been posted to the ISAC website for discussion.  If you go to http://www.isac-net.org/content/view/698/150/, you can post your opinion on the topics that have been formally proposed.  So far those are:
1. Using Zip as the ACS container file format
2. Using netCDF or FCS to contain the raw data
3. Using Gating-ML to contain information about data analysis, including gating, compensation and data transformation

What is the purpose of creating these standards?  Information about the machine would allow reviewers and emulators to understand and troubleshoot an experiment.  A text based method of preserving compensation matrices and gate locations, coupled with an open source raw data format, would allow an analysis performed on any software that conformed to the standard to be read and edited in any other conforming software.  The ability to freely pass analysis work to anyone with any analysis program, or to edit the outputs of any analysis software, create custom algorithms, and output results that can still be interpreted by the analysis software is the holy grail of flow cytometric data mining.  All of these standards are meant to be used to make it easier on users to document and share their experiments.