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| Workflow Made Simple, by John Quinn Ph.D. |
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As an application scientist with Treestar, I’m frequently asked for advice on how to make the workflow of cytometric experimentation easier. One of the simplest, yet most powerful methods for simplifying the process from collection through publication is proper annotation. The annotation I am referring to is the information needed to interpret and reproduce your experiment. The most efficient manner in which to do so is to...
The most efficient manner in which to do so is to fill out the appropriate keywords in your FCS files either during collection, or post collection using FlowJo. By including the information as keywords in the FCS file the data and the metadata, which is “data about the data”, will not become separated. If asked, most researchers would have to admit to frantically flipping through notebooks looking for a scrap of paper listing which antibodies were used in a particular experiment at some point in their career. But what constitutes the “appropriate” keywords? The ISAC (International Society for Analytical Cytology) data standards task force has produced an answer to this question. One of the projects of the task force, coordinated by Ryan Brinkman of the BC Cancer Research Centre and funded by an NIH grant, has been to create a document listing the Minimal Information for Reporting a Flow Cytometric Experiment (MIFlowCyt). It contains a list, with explanation, of each term should be reported to make an experiment reproducible. The document divides the terms into four categories: experimental overview, flow sample/specimen details, instrumentation details, and data analysis details. MIFlowCyt can be accessed from ISAC’s webpage. FCS files are not currently formatted to store all of the terms listed in MIFlowCyt. The plan for the next standard for flow data is to include all the MIFlowCyt information, but that’s an article for another day. At the moment, FCS files will store most of the terms specified in the flow sample/specimen details and instrumentation portions of MIFlowCyt, and I’ll encourage you to take advantage of this capability. MIFlowCyte normative standard proposal can be downloaded here . The MIFlowCyte wikipage can be found here For more on this topic, contact John Quinn, Ph.D. John Quinn, Ph.D. Application Scientist Tree Star, Inc. www.flowjo.com john@treestar.com |
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