Space Ranger v4.0 and later supports nucleus and cell segmentation for Visium HD and Visium HD 3' Spatial Gene Expression data with corresponding H&E microscopy images. The spaceranger segment pipeline was introduced so that users can assess Space Ranger's nucleus segmentation performance on a variety of H&E images before running the assay to inform experimental design and sample choice.
Only two parameters are required to run spaceranger segment, a unique job ID and a path to the H&E microscope image (see also the image recommendations page).
spaceranger segment --id=unique_job_id --tissue-image=path/to/image.tif
See the Space Ranger Commands page for more details on the full range of options available in spaceranger segment.
A successful spaceranger segment run concludes with a message similar to this:
Outputs:
- nucleus_instance_mask: /path/to/outs/nucleus_instance_mask.tiff
- nucleus_segmentations: /path/to/outs/nucleus_segmentations.geojson
- websummary: /path/to/outs/websummary.html
Waiting 6 seconds for UI to do final refresh.
Pipestance completed successfully!
The spaceranger segment pipeline outputs nucleus segmentation masks in TIFF and GeoJSON format that can be specified to spaceranger count. It is recommended to check the web summary first to assess quality control metrics. To continue, see Understanding Space Ranger Outputs.