Write Annotations to AnnData

[srivarra]

Annotations are saved in an AnnData object and then written to zarr.

Here is an example of this, annotation-specific AnnData object.

AnnData object with n_obs × n_vars = 18861 × 768
    obs: 'id', 'fov_name', 'track_id', 'parent_track_id', 'parent_id', 't', 'y', 'x'
    obsm: 'X_pca', 'X_phate', 'X_projections', 'X_umap'

You can access the observations Pandas DataFrame with adata.obs.

Embeddings are saved in obsm which is a Key-value store. For example you can access X_pca by running adata.obsm["X_pca"]

The feature matrix is saved as the main data array of the AnnData object, saved to .X.
Removes the / in FOV names, ("/B/1/000000" $\rightarrow$ "B/1/000000")

I tried using it with the current implementation of UMAP, but ran into some errors with n_neighbors so I added a quick kwarg fix.

Todos:

• Incorporate the tracking.csv from add percentiles to preprocessing #274? (I'm not entirely sure on this) - from this comment

[ziw-liu]

Is it easy to include a converter from the old format?

[srivarra]

Is it easy to include a converter from the old format?

Yes it's pretty straightforward. I'll add a function to do so.

[edyoshikun]

I suggest adding a simple script that shows how to use this for plotting the PCs or wrangling the new format. Once we have that converter, then we should be good to go.

[srivarra]

@edyoshikun Ready for re-review

[edyoshikun]

Im getting an error when loading the annotations. There is a mismatch in the embedding xarray fov_name and the annotation_df['fov_name']. The fov_name should not have the forward slash.

annotations_path = "/hpc/websites/public.czbiohub.org/comp.micro/viscy/DynaCLR_data/DENV/test/20240204_A549_DENV_ZIKV_timelapse/extracted_inf_state.csv"
embeddings_path = "/hpc/websites/public.czbiohub.org/comp.micro/viscy/DynaCLR_data/DENV/test/20240204_A549_DENV_ZIKV_timelapse/precomputed_embeddings/infection_160patch_94ckpt_rev6_dynaclr.zarr"

[ziw-liu]

Can we have tests for these functions?

[ziw-liu]

Can you add a test for the CLI?

[ziw-liu]

Test is failing because the function has the same name as the module (generally a thing to avoid).