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[BUG] Need to reimplement loading from a text file for cell detection #184

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adamltyson opened this issue Jun 10, 2021 · 2 comments
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[BUG] Need to reimplement loading from a text file for cell detection #184

adamltyson opened this issue Jun 10, 2021 · 2 comments
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See #182

Moving to using dask means that confusingly, if you have a text file of paths, the registration will work, but the cell detection wont.
@adamltyson adamltyson added bug Something isn't working good first issue Good for newcomers labels Jun 10, 2021
@adamltyson adamltyson self-assigned this Jun 10, 2021
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adamltyson commented Jun 18, 2021 •
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@stephenlenzi you mentioned you might take this on. This could also be an opportunity to extend support for different data types. Theoretically we could support anything, as now cellfinder-core only requires an array-like object.

This code might be better in imio though. Some ideas:

  • Path to directory of tiffs
  • Path to text file of tiffs
  • 3D tiff
  • h5/BDV
  • npy

npeschke added a commit to npeschke/cellfinder-core that referenced this issue Sep 15, 2021
@npeschke
fixing loading from txt file
79a0107 
hotfix for brainglobe/cellfinder#184
@npeschke npeschke mentioned this issue Sep 15, 2021
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@adamltyson adamltyson mentioned this issue Feb 9, 2024
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adamltyson pushed a commit to brainglobe/cellfinder-core that referenced this issue Sep 15, 2021
@npeschke
fixing loading from txt file with dask (#24)
e856c2c 
* fixing loading from txt file
hotfix for brainglobe/cellfinder#184

* added unittests for IO

* fixed side effect with tests searching for subdirectories
moved brain_paths.txt to brain directory
replaced paths with constants
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This issue is fixed for now by @npeschke in brainglobe/cellfinder-core#24.

Closing this issue, and moving to brainglobe/brainglobe-utils#36.

willGraham01 added a commit that referenced this issue Sep 1, 2023
@sfmig @willGraham01
asv benchmarks for imports and tools modules (#184)
90c6c25 
Co-authored-by: Will Graham <[email protected]>
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