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csv file for each sample and the name of the file matches the name of the sample, like the example data found here: If you haven't defined any cell types and you have a. Alternative Way to Import Multiple Samples The sample group and sample annotation currently have no functionality other than annotation. csv files representing empty cell gates exported from FlowJo, or if some samples have additional channels, CytoMAP will run into errors.
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This multi-sample import assumes all samples have the same number and type of cells, as well as the same channels. When finished renaming things, click the load button in the bottom left of the window. Rename any sample names or phenotype names as desired. csv files contained in those folders, using the file names to populate the sample and phenotype fields in the resulting import dialog box. This will scan each folder and open all of the.
![rename samples flowjo 10 rename samples flowjo 10](http://v9docs.flowjo.com/html/images/prefsworkspace.jpg)
Select each sample’s folder and click “Open”. This will bring up a dialog box asking the user to select the folders where the. csv files for each phenotype in each sample into a unique folder containing only that sample’s. To simultaneously import multiple samples into CytoMAP, first save all of the individual. The names of the channels/markers will be taken from the first row (header) of the. The name of the sample will be the common string among the four. The names of the cells will be the names of the. csv files, each containing columns of channel intensitiesĪnd rows of individual cell objects, CytoMAP will create one new sample with four cell types. If you use the 'load csv' function and select four. csv files will be treated as separate phenotypes. The data should be formatted as columns of parameters and rows of individual cells/objects. csv, with at least x-y positional data can be loaded into this program. Loading Data into CytoMAPīelow are the types of data that can be loaded into CytoMAP. To avoid errors when importing cells into CytoMAP, name each phenotype/.csv file and sample folder with a unique name. However, you can select multiple populations (‘ctrl’ + click) from the same sample and FlowJo will export them each to their own individual. Selecting a parent population will not automatically export all of the children populations. To export populations from FlowJo, select the populations of interest, right-click on the selected populations and select “Concatenate, export populations”.įor output choose the Scale values “channels” correspond to values which have been scaled by FlowJo, and “scale” corresponds to the raw data.Įach sample must be exported separately, ideally to a single folder for each sample. Often the step before importing any data into CytoMAP is exporting cell populations from FlowJo. This section discusses the various data types and formats that can currently be imported into CytoMAP.