commits

SHA	Message	Author	Date
1431911f	merge Merge pull request #363 from scverse/performance/xenium-points-parsing	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	7 months ago
3b756dab	faster xenium points parsing by precomputing categories	Luca Marconato <m**r@g**m>	7 months ago
785fa9a6	merge Merge pull request #360 from scverse/add-provenance-metadata	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	7 months ago
0a41aada	add spatialdata-io version and reader name to attrs	Luca Marconato <m**r@g**m>	7 months ago
fc5f3ca6	merge Merge pull request #357 from scverse/pre-commit-ci-update-config	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	7 months ago
8762f91b	merge Merge pull request #279 from lucas-diedrich/image-reader-chunkwise	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	7 months ago
355b6957	c=1 vs c=3 benchmark	Luca Marconato <m**r@g**m>	7 months ago
4b4a00e7	fix pre-commit	Luca Marconato <m**r@g**m>	7 months ago
163d8b04	benchmark for image() with synthetic data	Luca Marconato <m**r@g**m>	7 months ago
19df3253	improve chunks support	Luca Marconato <m**r@g**m>	7 months ago
2f541f3a	merge Merge pull request #349 from MSHelm/fix/macsima-cycle-parsing	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	7 months ago
a890951e	wip fix chunks	Luca Marconato <m**r@g**m>	7 months ago
597dc714	Clarify data format specification	Martin Helm <m**h@m**m>	7 months ago
5a20f413	fix pre-commit benchmark_image	Luca Marconato <m**r@g**m>	7 months ago
93554e7f	Clarify documentation	Lucas Diedrich <d**h@b**e>	7 months ago
21f8fc65	chore: Remove Note and TODO	Lucas Diedrich <d**h@b**e>	7 months ago
5d9ece29	[Fix] Shape dimensions were inversed. Fix shape specification and make it sel...	Lucas Diedrich <d**h@b**e>	7 months ago
2dabbf9f	Refactor chunk specification to follow (y, x) order and update related docume...	Lucas Diedrich <d**h@b**e>	7 months ago
a9c2a2bd	Follow standard convention of image dimensions throughout reader function. Sw...	Lucas Diedrich <d**h@b**e>	7 months ago
a2930d51	Add comment to clarify use of asymmetric chunk sizes in test_read_tiff	Lucas Diedrich <d**h@b**e>	7 months ago
14665967	[Test] Use small assymetric chunk sizes to capture any issues with the comput...	Lucas Diedrich <d**h@b**e>	7 months ago
395609a1	Handle some edge cases for files with invalid metadata	Martin Helm <m**h@m**m>	8 months ago
0c482acf	wip benchmark (bugs)	Luca Marconato <m**r@g**m>	8 months ago
7f5b7ce9	better docstring	Luca Marconato <m**r@g**m>	8 months ago
f7ad81aa	better english	Luca Marconato <m**r@g**m>	8 months ago
3b296da2	fix indices in _read_chunks()	Luca Marconato <m**r@g**m>	8 months ago
a6dc25fa	Fall back to MICS cycle ID if Cycle is not present in v0 metadata	Martin Helm <m**h@m**m>	8 months ago
dfb7d8ee	Use channel names as tie breaker to sort channels within same cycle	Martin Helm <m**h@m**m>	8 months ago
fc26342c	np._int -> np.number	Luca Marconato <m**r@g**m>	8 months ago
80a931d0	fix wrong dimension _compute_chunks(); cover with test	Luca Marconato <m**r@g**m>	8 months ago
a7a2b923	remove unused min_coordinate	Luca Marconato <m**r@g**m>	8 months ago
c14cb222	add test for dask-image fallback for compressed tiffs	Luca Marconato <m**r@g**m>	8 months ago
9d44f25e	fix transpose in image(); wip code review	Luca Marconato <m**r@g**m>	8 months ago
0f29d501	[pre-commit.ci] pre-commit autoupdate	pre-commit-ci[bot] <6**]@um> Committed by: GitHub <ny@g**m>	8 months ago
9f3cc3ce	fix pre-commit	Luca Marconato <m**r@g**m>	8 months ago
57055153	merge Merge branch 'main' into image-reader-chunkwise	Luca Marconato <m**r@g**m>	8 months ago
2ebfab02	merge Merge pull request #320 from Liripo/main	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
ff938906	fix docs	Luca Marconato <m**r@g**m>	8 months ago
6704bedb	merge add rgb parameter to to_legacy_anndata()	Luca Marconato <m**r@g**m>	8 months ago
35bd2da8	fill in missing urls, fix typo	Luca Marconato <m**r@g**m>	8 months ago
885ee416	fix 'on' config for github workflow	Luca Marconato <m**r@g**m>	8 months ago
c06b53f8	merge Merge pull request #356 from scverse/upload-macsima-ci-dataset	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
61147b0c	add macsima ci datasets	Luca Marconato <m**r@g**m>	8 months ago
d721a25d	add small OMAP ci datasets	Luca Marconato <m**r@g**m>	8 months ago
c367e628	merge Merge pull request #283 from scverse/bugfix/issue245-linearring	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
2445c76a	Add comprehensive metadata test	Martin Helm <m**n@b**g>	8 months ago
091c5f38	fix formatting	Luca Marconato <m**r@g**m>	8 months ago
57a1cb20	ehapes in xenium remove constrain on representation	Luca Marconato <m**r@g**m>	8 months ago
334fc55b	Harmonize imagetype between format versions. Adjust tests for small datasets ...	Martin Helm <m**n@b**g>	8 months ago
9768bfdb	fix	Luca Marconato <m**r@g**m>	8 months ago
2e228cf4	wip support for polygons with 3 vertices without filtering	Luca Marconato <m**r@g**m>	8 months ago
c0dcf5e9	merge Merge branch 'main' into bugfix/issue245-linearring	Luca Marconato <m**r@g**m>	8 months ago
6be72966	merge Merge pull request #347 from scverse/improve_legacy_adata_reader	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
6080158e	adjusted comment and logger	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
57005dd3	merge Merge branch 'main' into improve_legacy_adata_reader	Luca Marconato <m**r@g**m>	8 months ago
28d05a2d	merge Merge pull request #337 from marcovarrone/xenium-labels-dask	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
ada3cd36	fix pre-commit	Luca Marconato <m**r@g**m>	8 months ago
54a24a07	use zarr zipstores in xenium	Luca Marconato <m**r@g**m>	8 months ago
92a09ae4	add asv benchmarks	Luca Marconato <m**r@g**m>	8 months ago
d3a247c1	persistent extraction of .zarr.zip	Luca Marconato <m**r@g**m>	8 months ago
d1483112	merge Merge branch 'main' into xenium-labels-dask	Luca Marconato <m**r@g**m>	8 months ago
5f829f51	merge Merge pull request #268 from scverse/seqfish-v2-fixes	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
6592674a	update .gitignore; strict True in zip	Luca Marconato <m**r@g**m>	8 months ago
6f35514b	merge Merge branch 'main' into seqfish-v2-fixes	Luca Marconato <m**r@g**m>	8 months ago
904abfcb	Emitt warning when duplicate key with different value is found in OME metadata	Martin Helm <m**n@b**g>	8 months ago
26fb99b1	merge Merge pull request #354 from scverse/fix/steinbock	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
a2bb7fca	fix steinbock	Luca Marconato <m**r@g**m>	8 months ago
06400c43	merge Merge pull request #353 from scverse/fix/warning-default-visium-hd	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
d9e8cb70	fix warning visium hd when default value was set	Luca Marconato <m**r@g**m>	8 months ago
0aae9ce7	merge Merge branch 'main' into fix/macsima-cycle-parsing	Luca Marconato <m**r@g**m>	8 months ago
23bcb729	merge Merge pull request #352 from scverse/vhd_dataset_id	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
3c7425ed	fix tests, improve exception, add docstring	Luca Marconato <m**r@g**m>	8 months ago
9d856861	make sure fullres_image_file is a Path	Quentin Blampey <q**y@g**m>	8 months ago
8a77ef8d	better dataset_id inference and minor fullres image fix	Quentin Blampey <q**y@g**m>	8 months ago
d5fa3f2a	fix table -> tables cosmx()	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
2405ad63	merge Merge pull request #335 from scverse/pre-commit-ci-update-config	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
ffeeea21	[pre-commit.ci] pre-commit autoupdate	pre-commit-ci[bot] <6**]@um> Committed by: GitHub <ny@g**m>	8 months ago
80b63186	merge Merge pull request #351 from scverse/fix-xenium-tests-pyarrow	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	8 months ago
2621d4b9	use pyarrow 21 in tests to fix xenium bug	Luca Marconato <m**r@g**m>	8 months ago
cef71707	Add public OMAP data sets for testing and adjust tests	Martin Helm <m**n@b**g>	9 months ago
82d304f8	Parse all metadata from ome metadata, nothing from filename	Martin Helm <m**n@b**g>	9 months ago
8b49711f	Parse additional metadata from filename stored in ome tiff	Martin Helm <m**n@b**g>	9 months ago
5c588fcd	Parse cycle from ame in tiff metadata, not actual filename	Martin Helm <m**h@m**m>	9 months ago
3dd1cd92	adjusted logger import	Tim Treis <t**s@h**e>	9 months ago
5eac22c3	made reader more flexible	Tim Treis <t**s@h**e>	9 months ago
fb578461	merge Merge pull request #343 from scverse/fix/visium_hd_3.x	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	10 months ago
cd74ebdf	fix scalefactors error visium hd 3.x	Luca Marconato <m**r@g**m>	10 months ago
c3fc6863	remove pyarrow upper bound	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	10 months ago
55efc2ca	merge Merge pull request #328 from 10XGenomics/stephen/spaceranger4.0	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	10 months ago
5ea81899	merge Merge pull request #341 from scverse/fix_zarr_v3_visium_reader	LucaMarconato <2**o@um> Committed by: GitHub <ny@g**m>	10 months ago
20ca6303	[pre-commit.ci] auto fixes from pre-commit.com hooks	pre-commit-ci[bot] <6**]@u**m>	10 months ago
2d21dc85	fix table parameter visium reader	Luca Marconato <m**r@g**m>	10 months ago
301650ea	fix bug cli bin sizes	Luca Marconato <m**r@g**m>	10 months ago
b94f096e	fix min test small datasets	Luca Marconato <m**r@g**m>	10 months ago
1db1c01a	fix visium_hd cli	Luca Marconato <m**r@g**m>	10 months ago
644f8c71	merge Merge commit 'refs/pull/328/head' of https://github.com/scverse/spatialdata-i...	Luca Marconato <m**r@g**m>	10 months ago
032a9bdb	add deprecation warning for load_segmentations_only in visium_hd	Luca Marconato <m**r@g**m>	10 months ago
62c3f9fe	ruff	Stephen Williams <s**s@1**m>	10 months ago
0fe6b779	test precommit	Stephen Williams <s**s@1**m>	10 months ago
0d11d26c	revert python change and update pytest	Stephen Williams <s**s@1**m>	10 months ago

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