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BICCN / cell-locator

manually align specimens to annotated 3D spaces
https://cell-locator.readthedocs.io
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ENH: Add optional lims-specimen-kind parameter #214

Closed allemangD closed 2 years ago

allemangD commented 2 years ago

Resolves #213

See https://github.com/KitwareMedical/Slicer/commit/f81033d29c2f8f0373896652ebd0d9c432f2fe46

allemangD commented 2 years ago

Tested against the mock lims server; see changes in https://github.com/KitwareMedical/AllenInstituteMockLIMS/commit/88942bfa647ae487de6de35c57b4aecde3e734da

Both these commands (cell locations) interact with one annotation file:

build/Slicer-build/CellLocator \
  --lims-base-url 'http://localhost:5000/' \
  --lims-specimen-id 1234 \
  --lims-specimen-kind 'IVSCC cell locations' \
  --atlas-type ccf

build/Slicer-build/CellLocator \
  --lims-base-url 'http://localhost:5000/' \
  --lims-specimen-id 1234 \
  --atlas-type ccf

While this one (tissue review) interacts with a different annotation file:

build/Slicer-build/CellLocator \
  --lims-base-url 'http://localhost:5000/' \
  --lims-specimen-id 1234 \
  --lims-specimen-kind 'IVSCC tissue review' \
  --atlas-type ccf

The parameter is working as expected. Merging now.