Segmentation mask input with morphology_focus names that don't match spatialdata-io expected names #2
Description
I have this issue: scverse/spatialdata-io#325 (comment) and someone suggested scverse/spatialdata-io#312 would have addressed it but it isnt working for me.
Until spatialdata-io fix the code, we need a work around. I think that would be renaming all the files in the output manually and then creating a new morphology.ome.tif file. I tried renaming the files from the names that come off the machine to the ones spaitaldata-io expects, however I'm still getting an error. It seems that there is some link between the names in the morphology_focus dir and morphology.ome.tif file.
I think the temp work around could be
- Rename the files in morphology_focus dir
- Create a new morphology.ome.tif and overwrite the old one using the renamed files in morphology_focus dir
This needs to be done for every ROI/sample (i.e every folder because each sample has its own folder with the layout below)
.
├── analysis
│ ├── clustering
│ ├── diffexp
│ ├── pca
│ └── umap
├── analysis_summary.html
├── analysis.zarr.zip
├── aux_outputs
│ ├── background_qc_images
│ ├── morphology_focus_qc_masks
│ ├── morphology_fov_locations.json
│ ├── overview_scan_fov_locations.json
│ ├── overview_scan.png
│ └── per_cycle_channel_images
├── cell_boundaries.csv.gz
├── cell_boundaries.parquet
├── cell_feature_matrix
│ ├── barcodes.tsv.gz
│ ├── features.tsv.gz
│ └── matrix.mtx.gz
├── cell_feature_matrix.h5
├── cell_feature_matrix.zarr.zip
├── cells.csv.gz
├── cells.parquet
├── cells.zarr.zip
├── experiment.xenium
├── gene_panel.json
├── metrics_summary.csv
├── morphology_focus
│ ├── ch0000_dapi.ome.tif
│ ├── ch0001_atp1a1_cd45_e-cadherin.ome.tif
│ ├── ch0002_18s.ome.tif
│ └── ch0003_alphasma_vimentin.ome.tif
├── morphology.ome.tif
├── nucleus_boundaries.csv.gz
├── nucleus_boundaries.parquet
├── transcripts.parquet
└── transcripts.zarr.zip