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Merged
merged 33 commits into from
Nov 8, 2025
Merged

temp PR: Visium HD 4.0 #333

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b1e6d06
feat: suppor for spaceranger4.0
stephenwilliams22 Sep 24, 2025
a6d7e9f
make nuc segmentation and cut dup code
stephenwilliams22 Oct 2, 2025
31379c8
use only in_nucleus
stephenwilliams22 Oct 2, 2025
34ac722
make local functions
stephenwilliams22 Oct 2, 2025
b7848fa
ruff
stephenwilliams22 Oct 6, 2025
ae43fe7
typing
stephenwilliams22 Oct 6, 2025
31c76fd
nuc seg cli
stephenwilliams22 Oct 7, 2025
9134c94
tests
stephenwilliams22 Oct 8, 2025
42028ce
add vignette
stephenwilliams22 Oct 10, 2025
b269d32
update BARCODE_MAPPINGS_PATH and calc centroids
stephenwilliams22 Oct 10, 2025
0e891ec
delete vignette. moved to new PR
stephenwilliams22 Oct 13, 2025
c9674ca
Merge branch 'main' into stephen/spaceranger4.0
LucaMarconato Oct 22, 2025
49d3e7e
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 22, 2025
30e4076
wip code review visium hd
LucaMarconato Oct 24, 2025
cc9dc68
wip code review
LucaMarconato Oct 24, 2025
e5c2d16
initial review pass
LucaMarconato Oct 24, 2025
ab3611b
Merge branch 'main' into stephen/spaceranger4.0
LucaMarconato Oct 27, 2025
8cecbf3
pin pyarrow
LucaMarconato Oct 27, 2025
4b8a41f
fix docstring
LucaMarconato Oct 27, 2025
39ffde5
code review simplification
LucaMarconato Oct 27, 2025
01583e0
fix typo
LucaMarconato Oct 27, 2025
8bb3ab9
fix unnecessary check
LucaMarconato Oct 27, 2025
3098486
fix unnecessary check
LucaMarconato Oct 27, 2025
955a9a6
fix docstring
LucaMarconato Oct 27, 2025
6f6459c
update tests
stephenwilliams22 Oct 29, 2025
0d11d26
revert python change and update pytest
stephenwilliams22 Oct 29, 2025
0fe6b77
test precommit
stephenwilliams22 Oct 29, 2025
62c3f9f
ruff
stephenwilliams22 Oct 29, 2025
032a9bd
add deprecation warning for load_segmentations_only in visium_hd
LucaMarconato Nov 3, 2025
644f8c7
Merge commit 'refs/pull/328/head' of https://github.com/scverse/spati…
LucaMarconato Nov 3, 2025
1db1c01
fix visium_hd cli
LucaMarconato Nov 3, 2025
b94f096
fix min test small datasets
LucaMarconato Nov 3, 2025
301650e
fix bug cli bin sizes
LucaMarconato Nov 3, 2025
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Merge branch 'main' into stephen/spaceranger4.0
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@LucaMarconato
LucaMarconato committed Oct 27, 2025
commit ab3611b3dfbc11980bd2c4f713a86aa70d920619

This merge commit was added into this branch cleanly.

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