Reports and exports

Write a report for a sample, copy or export plots, and export unmixed FCS files.

From your unmixed data, Honeychrome can:

• write a sample report as a Word (DOCX) file;
• copy or export any plot as an image;
• export unmixed FCS files for a folder of samples.

To compare samples with charts, see Simple Stats.

Sample report

Select a sample in the sample browser and click the DOCX button on the toolbar, or choose File > Generate Sample Report.

• The report can include the raw data, the spectral process and the unmixed data for that sample. By default it has the unmixed data and the spectral process; choose what to include in Edit > App Configuration.
• It is saved in the experiment’s Reports folder, in subfolders that mirror the Raw folder.
• Figures and tables can be copied from the report into other documents.

Copy or export a plot

Right-click a plot to copy it to the clipboard or export it as a PNG file.

Export unmixed FCS files

Choose File > Batch Export FCS Files, or use the toolbar button.

1. Choose the folder of samples to export.
2. Optionally tick Subsample before exporting. The number of events kept is set in Edit > App Configuration (10,000 by default).
3. Click Proceed.

Each sample is unmixed and written as a new FCS file in the experiment’s Unmixed folder, in the same subfolders as the raw data.

• Samples are unmixed with the experiment’s method: per-cell autofluorescence, the noise model or the spectral variants, with spectral corrections if you use them (see AutoSpectral in Honeychrome).
• The spillover written to the files is your fine-tuning matrix.
• Large files are exported in chunks to limit memory use. Exports with spectral variants start with a time estimate.

Your raw FCS files are never changed; they stay in the Raw folder.

An export is a long job, so other long calculations wait until it has finished; see Long jobs.

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