vscode-fcs-viewer
Inspect flow cytometry data from FCS files in VS Code.
This extension was almost exclusively vibe-coded with claude-code.
I don't guarantee for its correctness, but its fun to play around with.
Features
- FCS Parser: Open and inspect FCS files.
- Plot Cards: Interactive Scatter Plots, Contour Plots, and Histograms cards thanks to
React and plotly-js.
- Compensation: Optionally apply the spillover compensation from the files
$SPILLOVER metadata key.
- Overview and table: All metadata, per-channel statistics, the spillover matrix, and a event table.
- Dimensionality Reduction: Visualization of high-dimensional cytometry data via UMAP provided by
umap-js.
- Save and load workspaces: Save plot configurations as a workspace and come back to it later.
Commands
FCS Viewer provides 3 commands to manage workspaces:
| Command |
Does |
Open Workspace… |
Pick a saved workspace, or start a new empty one |
Save Workspace… |
Name the current workspace's samples and plot cards |
Discard Workspace… |
Delete a saved workspace; the FCS files are untouched |
Right-clicking a .fcs file adds Open in FCS Viewer (always a new
workspace) and, when one is already open, Add to FCS Viewer Workspace.
Settings
| Setting |
Default |
Meaning |
fcsViewer.defaultSampleSize |
5000 |
Events plot cards render by default |
fcsViewer.defaultCofactor |
0 |
Arsinh cofactor; 0 picks from $CYT |
fcsViewer.maxFileSizeMB |
1024 |
Prompt before opening larger files |
fcsViewer.maxSliceMB |
16 |
Confirm before transferring more than this |
Limitations
- Gating: Gating is currently not supported.
- Editing: The extension is currently read-only and never writes to your FCS files.
- t-SNE: UMAP was preferred over t-SNE for efficiency.
Acknowledgements
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