Skip to content

read AnnData-zarr tables directly - #130

Merged
Artur-man merged 10 commits into
HelenaLC:mainfrom
Artur-man:readbasilisk
Mar 29, 2026
Merged

read AnnData-zarr tables directly#130
Artur-man merged 10 commits into
HelenaLC:mainfrom
Artur-man:readbasilisk

Conversation

@Artur-man

@Artur-man Artur-man commented Jan 29, 2026

Copy link
Copy Markdown
Collaborator

This fixes unnecessary basilisk-based spatialdata read_zarrs, and instead reads each anndata-zarr table directly.
Potentially fixes #124, and other errors caused by trying to read the entire spatialdata object on py.

@Artur-man

Copy link
Copy Markdown
Collaborator Author

Although the current upgrade to the recent version of SpatialData solved the reader issue, reading anndata tables only might still performance faster. Thus, lets keep this PR open for now.

@Artur-man
Artur-man merged commit b7a6daa into HelenaLC:main Mar 29, 2026
3 of 4 checks passed
@Artur-man
Artur-man deleted the readbasilisk branch March 29, 2026 14:52
HelenaLC pushed a commit that referenced this pull request Jul 5, 2026
read AnnData-zarr tables directly

Former-commit-id: b7a6daa
Former-commit-id: 4790f871c6158ff37df2eb5427ad74e5635a29a2
Artur-man added a commit to Artur-man/spatialdataR that referenced this pull request Aug 15, 2026
read AnnData-zarr tables directly

Former-commit-id: b7a6daa
Former-commit-id: 4790f871c6158ff37df2eb5427ad74e5635a29a2
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Error opening zarr store

1 participant