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Read anndata as napari points and tracks #81

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@will-moore will-moore commented Mar 3, 2023

NB: this PR requires ome/ome-zarr-py#256
TODO: Once that PR has been merged and released, need to bump the requirement version for ome-zarr here.

This uses code borrowed from @kkyoda at https://github.com/openssbd/bdz/ to translate anndata tables into napari points and tracks.
AnnData tables must be in the format generated by openssbd/bdz#2
NB: the spec for tables is currently open PR at ome/ngff#64

To test:

$ napari wt-N2-081015-01.ome.zarr --plugin napari-ome-zarr

Screenshot 2023-03-03 at 10 15 57

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will-moore commented Mar 9, 2023

@kkyoda - I've played around quite a bit with the anndata_to_napari_tracks() login here to try and get it to comply with the style of tracks expected by the "arboretum" plugin: https://www.napari-hub.org/plugins/napari-arboretum.
E.g. see example at https://raw.githubusercontent.com/lowe-lab-ucl/btrack-examples/main/examples/tracks.csv

This expects each point to only be in 1 track, and uses a "graph" dictionary to link the tracks.
I've also tried to handle cases of 2 or more tracks merging into 1.

With these changes, you can now view the lineage of the tree:

Screenshot 2023-03-09 at 09 59 31

@will-moore will-moore force-pushed the tables_to_napari_tracks branch from fa2b567 to 666989c Compare March 9, 2023 11:01
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Codecov Report

Patch coverage: 17.85% and project coverage change: -16.20 ⚠️

Comparison is base (0da60a2) 87.56% compared to head (eb9de1a) 71.36%.

Additional details and impacted files
@@             Coverage Diff             @@
##             main      #81       +/-   ##
===========================================
- Coverage   87.56%   71.36%   -16.20%     
===========================================
  Files           3        4        +1     
  Lines         185      241       +56     
===========================================
+ Hits          162      172       +10     
- Misses         23       69       +46     
Impacted Files Coverage Δ
napari_ome_zarr/table_utils.py 16.32% <16.32%> (ø)
napari_ome_zarr/_reader.py 84.76% <28.57%> (-4.02%) ⬇️

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Closing since ome/ngff#64 is closed

@will-moore will-moore closed this Oct 24, 2023
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