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Annotate .fcs files with gated population classification

Hi,

I have a .fcs file that I can process with FlowJo. Here I can set gates and name these after the population the cells in these gates represent. I would like to export that classification for each cell. The simplest solution would therefore be to add the string column 'population' to the cell .fcs data that specifies the population it belongs to. Also possible would be to add a column for each gate and mark with a boolean if the cell is inside or outside that gate. However, I have not found software that has this function to export gating annotations for each cell. Do you know software tools for that?

facs flow cytometry flowjo
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updated by Dylan • Dylan • written by Benni • Benni

1 answer

It has been a few years since the original post but I wanted to let anyone who finds this know that FlowJo has a plugin called "Labeler" for FlowJo version 10 that allows users to embed information about gate ownership on a per cell basis into the fcs file.

For each population, Labeler creates a new binary parameter indicating wether or not a cell is within a population in FlowJo. A value of 0 indicates that the cell is not in the population and a value of 1 indicates the cell is in the population. The parameter(s)created by Labeler can then be exported as part of the fcs file and can convey this population ownership in other fcs files.

To obtain this plugin, email FlowJo@bd.com and they can send you a link to the tool as well as an explanation video further demonstrating how to use it.

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written by Dylan • Dylan

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