[main] Feature/spatialdata support#53
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Trimmed copy of the spatialdata writer introduced in PR #37 (commits e4e8846 + c26dd83 + bdec108 by @enric-bazz). Strips the delaunay boundary path and unused convenience helpers; inlines require_spatialdata to avoid the optional_deps refactor. Original-author: enric-bazz <enrico.bazzacco02@outlook.it>
Adds --save-spatialdata and --boundary-method CLI flags (under the existing I/O group) and threads them through ISTSegmentationWriter to emit a SpatialData zarr store next to the AnnData output. Adds the 'spatialdata' optional dependency. Integration shape taken from PR #37 commit f99b3fb by @enric-bazz, narrowed to the output path only (no loader, no 3D, no QV filter, no logging refactor). Original-author: enric-bazz <enrico.bazzacco02@outlook.it>
Tobiaspk
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I'm unable to install spatialdata into the same environment. Anyhow, it appears that the spatialdata construction takes a long time, even for a small dataset. Might need more robust installation instructions and profiling still. |
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Just noticed that anndata creation uses |
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Support Spatialdata writer. Adapted from #37 @enric-bazz
Introduces two new CLI parameters:
--save-spatialdataboolean--boundary-methodone of {input, convex_hull, skip}Changes to the original PR:
delauney. This would add 500+ lines of source code. Please share if there is an argument to keep it.optional_deps.py(now inline), other heavy edits to data_module, preprocessor etc. Only includes functions to write a Spatialdata.TODOs:
write_anndata. This reduces duplicate code. Also, the current implementation forgets to filter by segger_similarity threshold. See [integration/peerlab] Bugfix/writing anndata #43 .boundary_methodtospatialdata_boundary_methodto make it clear that this relates to the spatialdata output, not to cell expansion or anything!