Import files and organize samples

Prepare your files

Use the original FCS files from your cytometer when available. Keep controls and experimental samples together, with filenames that identify the sample. The workspace uploader also accepts LMD, CSV, TSV, TXT, Parquet, and ZIP files. A summary table of population percentages belongs in the assay workflow; it does not contain the individual events needed for gating.

If you are moving an analysis from FlowJo, keep the original event files as well as the .wsp file. A workspace describes the analysis and references its samples; it does not replace the event data.

Create a workspace and import

1. Open Flow cytometry from the header and create or select a workspace for the experiment.
2. Upload your sample files using the workspace import area. Wait for each file to finish processing before opening its plots.
3. Check the sample names, event counts, and channel metadata. Confirm that detector names and marker labels match the panel you acquired.
4. Add sample annotations and groups for conditions, donors, or time points. Use these groups when comparing samples later.

Check the first sample

Open a sample in the gating workbench. Confirm its identity and event count before drawing gates. Inspect the scatter channels, fluorescence channels, and compensation settings. Resolve unexpected channel names or missing parameters before applying a strategy to other samples.

If an import fails

Read the error for the affected file. Check that the file is complete and that its contents match its extension. For tabular event data, confirm that channel columns contain numeric measurements. Retry a single file to isolate the problem; keep the original file unchanged.

If a FlowJo import reports missing samples or channel mismatches, correct the sample mapping and review the import report before continuing.

Import acceptance checklist

1. Confirm each expected experimental sample and control appears once in the workspace.
2. Compare event counts and parameter names with the source acquisition record. Investigate empty files or missing channels before gating.
3. Check annotations for sample identity, condition, donor, and acquisition batch. Keep identifiers consistent across uploads.
4. Open representative samples and controls in the workbench and confirm that the displayed data is from the intended file.

Tabular event data and metadata

For event tables, each row must describe an event and each channel column must describe a measured parameter. Keep summary rows and population percentages out of an event table. Confirm which columns were imported as channels.

Tabular conversion can lose acquisition metadata present in an FCS file. Record compensation and transform settings separately when that metadata is absent; do not infer that a text export contains the same analysis context as the original FCS.

Preserve an import record

Keep the source filenames, workspace identifier, acquisition notes, and any import warnings together. If you replace an incomplete file, identify which sample is the accepted version before propagating gates or collecting statistics.