Import a FlowJo workspace

Keep the source files together

Prepare the FlowJo .wsp file and the FCS files it references. The importer reconstructs supported gates, transforms, compensation, and sample structure. File-specific features may need adjustment; importing a workspace is not a guarantee that every result matches the original.

Import and inspect

1. Open FlowJo import and select or drop the .wsp file.
2. Read the import report. Review unsupported features, warnings, and sample or channel mapping issues before opening the reconstructed analysis.
3. Provide the matching event data as prompted. Check the sample identity and parameter mapping rather than relying on the filename alone.
4. Open the imported analysis and inspect its gating tree, compensation, and transforms. Compare representative population counts and frequencies with the original analysis.

Investigate differences

Start with the same source events. Then compare the parent population, gate geometry, channel mapping, transform settings, and compensation. A difference earlier in a gating hierarchy can affect every descendant.

Resolve warnings explicitly. Do not treat a reconstructed gate as verified just because it appears on a plot. For unsupported features, document any replacement or manual adjustment you make.

Continue the analysis

Save the reviewed analysis in Gradiance before making further changes. Preserve the original .wsp and FCS files as a reference. If you export a workspace back to FlowJo, inspect that export in the destination application before relying on it.

Build a comparison record

1. Choose the same original FCS file in both applications and confirm the total event count.
2. Compare the gate hierarchy from the root downward, recording each population name, parent, count, and frequency denominator.
3. Check compensation, channel mapping, and transforms at the first point where counts differ.
4. Record warnings, unsupported features, and manual replacements from the import.
5. Preserve the source workspace and a reviewed Gradiance analysis with the comparison notes.

Decide whether the import is ready to use

Define the acceptance criteria for your experiment before relying on imported results. Include the populations that matter to your question and explain any differences you accept. A successful import only establishes that the file was processed.

If a required feature cannot be reconstructed or a population discrepancy remains unexplained, keep that result marked for review. Share the import warning and a minimal reproducible sample with support rather than assuming a visually similar boundary is equivalent.