SituCraft

Exports

Any segmentation of a dataset exports for other tools, into one folder: SpatialData and AnnData Zarr, Parquet and CSV, Matrix Market, GeoJSON, or Xenium Ranger's inputs with the command. Every file is listed by its SHA-256.

The formats

The Segmentation view's Export a segmentation: the formats chosen, the folder, and an export of the Lung example's instrument segmentation listed with its files and the prepared Xenium Ranger commandThe Segmentation view's Export a segmentation: the formats chosen, the folder, and an export of the Lung example's instrument segmentation listed with its files and the prepared Xenium Ranger command
An export of the Lung example's instrument segmentation, with its files and the prepared Xenium Ranger command.

Export a segmentation writes any of a dataset's segmentations for other tools, into one folder you name:

FormatForHolds
SpatialData Zarrspatialdata, napari-spatialdataThe cells as a label image and as polygons, the transcripts as points with their cells, the counts as an AnnData table
AnnData Zarrscanpy, anndataThe counts, with each cell's measures and centroid
Parquet; CSVDuckDB, pandas, R, polarsCells, transcripts with their cells, outlines and counts, in Xenium's column names
Matrix MarketSeurat (Read10X), scanpyThe counts as Xenium and Cell Ranger write them
GeoJSONQuPath, GIS toolsEach cell's outline as a polygon naming it
Xenium Ranger inputsXenium Ranger's import-segmentationThe cells and nuclei as label masks on the morphology image's pixels, and the command

What an export keeps

Coordinates are in µm. Beside the files, situcraft-export.json says what was exported, from what and by which SituCraft, lists every file by its SHA-256, and gives fingerprints of the label image, the counts and the transcripts' cells that every format holds the same (Formats), so that you can check any reader got it exactly. The export runs as a job, is written under a temporary name and renamed into place when complete, and is recorded in the project. A folder that exists is replaced only when you ask, and only when it is an earlier SituCraft export.

For Xenium Ranger

For Xenium Ranger, SituCraft prepares the inputs and the command, and does not run it. It checks first that the masks are the morphology image's size, which cells have no pixel (Xenium Ranger cannot keep them), and how many transcripts this segmentation assigns otherwise than its mask holds at their pixel (Xenium Ranger assigns by the mask). Copy the command puts it on the clipboard to run where Xenium Ranger is installed.