FLIMKitPlugins / FLIMKit / Outputs and File Formats · edit on GitHub
Outputs & File Formats
| Format | Description |
|---|---|
| PNG | Intensity and lifetime map images for quick visualisation |
| OME-TIFF | Lossless, metadata-preserving export, opens correctly in Fiji/ImageJ |
| OME-Zarr | Lossless and compressed, one channel per exported map, OME-NGFF 0.4 |
| GeoJSON | ROI geometries and statistics, imports directly into QuPath |
| CSV | Fit summaries and per-ROI statistics |
| NPZ | Session files (fitting results, phasor arrays, cursor state) for session restoration |
| NPY | Raw FLIM histogram cubes and assembled lifetime maps |
| TXT | Human-readable fit summaries |
OME-Zarr export
Export Images offers OME-Zarr alongside PNG and OME-TIFF. It writes one store
holding a single (c, y, x) float32 array, with each image you ticked as a
named channel, so intensity and lifetime end up as two channels of the same
image rather than two files. Channel names, the pixel size and the summed-fit
results are written into the store metadata: the fit summary sits under the
flimkit key in .zattrs, so the numbers travel with the image.
The store is named after the scan, R146_FOV1.ome.zarr for R146_FOV1.ptu,
falling back to results.ome.zarr when there is no input path to take a name
from. Exporting several fields of view into one folder therefore leaves one
store per field rather than overwriting.
The layout is OME-NGFF 0.4 on a Zarr v2 store, which is the version the
readers in Fiji, napari and QuPath are written against. The store validates
against the ome-zarr-models 0.4 schema and reads back through the reference
ome-zarr reader with its channel names and axes intact; I have not opened one
in Fiji, napari or QuPath myself. Chunks are compressed with Blosc/zstd, which
is where the size saving comes from: on a 512 square float32 intensity and
lifetime pair the store is about a third of the two uncompressed OME-TIFFs.
Zarr is a base dependency, so nothing extra needs installing and the compiled application carries it. If it is somehow missing the export dialog says so and does nothing rather than writing a partial store.