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Plot tracks in latent space and real space #135

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merged 9 commits into from
Aug 17, 2024
Merged

Plot tracks in latent space and real space #135

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5be72cd
slice by FOV and track
mattersoflight Aug 15, 2024
aaa9191
proper indexing
mattersoflight Aug 15, 2024
1982f92
plot features of a single track
mattersoflight Aug 15, 2024
392a674
rename (dataset -> embedding_dataset)
mattersoflight Aug 15, 2024
4a01590
trying to read patches of a track
mattersoflight Aug 15, 2024
1debe64
display cells from the chosen track in napari
mattersoflight Aug 15, 2024
d8b2b2f
project a track on umap computed from all features
mattersoflight Aug 16, 2024
faf26a2
Animated latent space (#137)
ziw-liu Aug 16, 2024
cbf280f
PCA of features and projections
mattersoflight Aug 17, 2024
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7 changes: 7 additions & 0 deletions applications/contrastive_phenotyping/contrastive_cli/plot_embeddings.py
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Expand Up @@ -16,6 +16,13 @@
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dataset

# %%
# Extract a track from the dataset
all_tracks_FOV = dataset.sel(fov_name=slice("A/4/0"))
a_track_in_FOV = all_tracks_FOV.sel(track_id=slice(23))
print(a_track_in_FOV.sizes())
# Why is sample dimension ~22000 long after the dataset is sliced by FOV and by track_id?
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# %%
# load all unprojected features:
features = dataset["features"]
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