scverse spatialdata issues

scverse / spatialdata

An open and interoperable data framework for spatial omics data

https://spatialdata.scverse.org/

BSD 3-Clause "New" or "Revised" License

168 stars 34 forks source link

issues

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Something wrong about annotating regions of interest with napari

#551 Tony4709 opened 3 days ago
0
update codecov

#550 giovp opened 4 days ago
0
Extract Image features from VisiumHD and Squidpy

#548 sokratiag opened 1 week ago
1
Overlay custom shape onto cell boundaries from Xenium

#547 EST09 opened 1 week ago
2
Cannot aggregate Labels2DModel by ShapesModel

#546 GuoshengMa opened 1 week ago
1
drop unmaintained pygeos for shapely 2.0

#545 omsai opened 1 week ago
4
Persist color channels in `rasterize()`

#544 clwgg opened 2 weeks ago
0
[pre-commit.ci] pre-commit autoupdate

#543 pre-commit-ci[bot] closed 5 days ago
0
Prototype/geoparquet

#542 LucaMarconato opened 2 weeks ago
0
Feedback on concatenate()

#541 grst opened 2 weeks ago
1
`polygon_query()` cannot filter the table for CODEX data

#540 GuoshengMa closed 1 week ago
15
Extract coordinates of shape after transformation

#539 EST09 closed 3 weeks ago
1
Think I'd just made a mistake but can't delete sorry

#538 EST09 closed 3 weeks ago
0
Extending get_values() for tables annotating points

#537 dylanclam12 opened 3 weeks ago
0
Invalid TIFF header

#536 minhtien-trinh closed 3 weeks ago
4
Utils to turn all transformations to affine

#535 LucaMarconato closed 3 weeks ago
1
Parameter name `(target_|to_)?coordinate_system(s)?`

#534 LucaMarconato opened 3 weeks ago
0
Order of tutorial notebooks

#533 Zethson closed 3 weeks ago
3
Error with `polygon_qurey()` function

#532 GuoshengMa closed 3 weeks ago
6
Failing join when index values are not unique

#531 melonora closed 3 weeks ago
2
fix models docstrings

#530 LucaMarconato closed 4 weeks ago
1
Mixed polygon/multipolygon geometry types from disk

#529 LucaMarconato opened 4 weeks ago
0
Raster models validation should be a `classmethod`.

#528 LucaMarconato opened 4 weeks ago
0
Missing `dtype` validation for labels?

#527 LucaMarconato opened 4 weeks ago
0
Incremental io

#525 ArneDefauw opened 1 month ago
0
Error in `add_shapes()` function

#524 GuoshengMa closed 1 month ago
2
fixes on docs, updated notebooks

#523 LucaMarconato closed 1 month ago
0
`_get_unique_label_values_as_index()` should be included as a case of `get_values()`

#522 LucaMarconato opened 1 month ago
0
Allow reloading of particular elements, and add `reload: bool` parameter to write functions

#521 LucaMarconato opened 1 month ago
0
refactoring join

#519 LucaMarconato closed 1 month ago
1
Cannot import ensure_warnings from xarray

#518 aeisenbarth closed 1 month ago
1
update image IO to write and read omero metadata correctly

#517 giovp opened 1 month ago
2
ValueError: '_index' is a reserved name for dataframe columns when writing multiple tables in Zarr

#516 Bisho2122 closed 1 month ago
2
update test read write on disk

#515 ArneDefauw closed 1 month ago
3
Update release.yaml

#514 LucaMarconato closed 1 month ago
0
test

#513 LucaMarconato closed 1 month ago
1
Join outside sdata

#512 melonora closed 1 month ago
2
[pre-commit.ci] pre-commit autoupdate

#511 pre-commit-ci[bot] closed 1 month ago
1
add static set annotation

#510 melonora closed 1 month ago
1
Update build.yaml to use setup-python v4

#509 LucaMarconato closed 1 month ago
4
fix ambiguous table vector None

#508 melonora closed 1 month ago
1
Different cell ids selected in regions: spatialdata vs Xenium explorer

#507 EST09 opened 1 month ago
4
minor fixes aggregate (.buffer() resolution), model dtype

#506 LucaMarconato closed 1 month ago
0
Parse and validate against `POLYGON Z` (same for points and multipolygons) in the `ShapesModel`

#505 LucaMarconato opened 1 month ago
0
Check for uniqueness of names also across the file storage

#504 LucaMarconato opened 1 month ago
0
Proposal: simplify data model for Points

#503 LucaMarconato opened 1 month ago
1
spatialdata-plot documentation hyperlink

#502 Artur-man closed 1 month ago
1
reimplemented incremental io

#501 LucaMarconato opened 1 month ago
11
`get_extent()` does not recognizes `SpatialData` in the single dispatch pattern in specific cases

#500 LucaMarconato closed 1 month ago
1
Custom spatialdata.models.ShapesModel throws "tuple index out of range"

#499 Artur-man closed 1 month ago
2