Data Import & Export
FCS file import
Cytomaton supports FCS 2.0, 3.0, and 3.1 files from any cytometer brand:
| Brand | Instruments |
|---|---|
| BD | FACSDiva, FACSymphony, LSRFortessa |
| Cytek | Aurora, Northern Lights |
| Beckman Coulter | CytoFLEX, Navios |
| Sony | ID7000, SA3800 |
Marker names are displayed immediately (CD3 FITC, not FL1-A). Spectral FCS files are auto-detected with an unmixing setup prompt.
Maximum file size: 2 GB per FCS file, up to 10M events.
FlowJo workspace import
Import FlowJo .wsp workspace files to bring your existing gating strategies into Cytomaton. The gate hierarchy is imported as a Cytomaton template — no rebuilding from scratch.
This is the fastest way to migrate existing analysis workflows from FlowJo.
Export formats
| Format | Details |
|---|---|
| PNG | 300 DPI, publication-ready with axis labels |
| SVG | Vector format for scalable figures |
| Publication-ready with gating strategies | |
| PowerPoint (.pptx) | 16:9 slides, white background, editable statistics tables |
| GraphPad Prism (.pzfx) | Column, Grouped, or XY layouts; defaults to % parent |
| CSV | Statistics table export |
| Clipboard (TSV) | Tab-delimited paste into Excel/Prism |
| MIFlowCyt (XML/JSON) | Pre-filled metadata for NIH DMS Policy compliance |
| ZIP | Export all as named ZIP archive |
All figure exports use proper biexponential (logicle) axis transforms with metadata annotations for reproducibility.
MIFlowCyt metadata export
Cytomaton generates pre-filled MIFlowCyt-compliant metadata from your experiment data for NIH DMS Policy compliance.
Covers 4 required domains: experiment overview, sample, instrumentation, and data analysis. Fields are pre-filled from FCS file headers, gating hierarchy, and compensation matrices. A completeness summary shows how many fields are pre-filled and which require manual entry.