Kevin Stachelek whtns
whtns
/ fix_tiff_ome_xml.py
Last active
October 7, 2025 17:40
Rename xenium ome.tiff files with a new naming pattern in morphology_focus for input into spatialdata
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| #!/usr/bin/env python3 | |
| """Rename morphology_focus OME-TIFFs and update OME-XML in TIFF comments. | |
| This script reads a simple mapping file (default: data/xenium_output_format.md) | |
| containing lines like: | |
| morphology_focus_0000.ome.tif: DAPI image | |
| It will scan the `morphology_focus` folders under the data directory, plan | |
| renames based on the mapping, optionally perform backups, rename files, and |