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gustaveroussy
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sopa
Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
https://gustaveroussy.github.io/sopa/
BSD 3-Clause "New" or "Revised" License
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Classifying positive cells
#83
dylanmr
closed
1 week ago
6
Dev
#82
quentinblampey
closed
2 weeks ago
0
Advice on simple IF hystocytometry
#81
cstrlln
closed
2 weeks ago
11
[Bug] sopa-v1.0.14 errors on Xenium v2 + multimodal cell segmentation data but not dapi-only data
#80
sooheelee
opened
3 weeks ago
5
Filtering by qv score for Xenium datasets
#79
saito-k1
closed
3 weeks ago
1
Immunofluorescence Image Segmentation
#78
suhridbuddha
opened
3 weeks ago
1
Two questions about the Baysor pipeline
#77
pakiessling
closed
3 weeks ago
5
Comseg cli
#76
tdefa
opened
3 weeks ago
6
sopa.segmentation.baysor.resolve error: Raise ValueError('negative column index found') ValueError: negative column index found
#75
mamyAndrianteranagna
closed
5 days ago
3
comseg_patch update and api_tuto"
#74
tdefa
closed
3 weeks ago
0
Visium HD support
#73
quentinblampey
opened
1 month ago
0
Dev
#72
stergioc
closed
1 month ago
0
WSI tile gathering optimizations
#71
stergioc
closed
1 month ago
0
WSI processing updates
#70
stergioc
closed
1 month ago
1
Dev
#69
quentinblampey
closed
1 month ago
0
Xenium Input File Change
#68
saito-k1
closed
1 month ago
6
[advice]Cellpose troubleshooting
#67
cstrlln
closed
1 month ago
3
Dev
#66
quentinblampey
closed
1 month ago
0
snakemake pipeline on subset of FOVs
#65
cstrlln
closed
1 month ago
18
sdata object has no cellpose or baysor boundaries
#64
altunbulakli
opened
1 month ago
10
CosMx input file format requirements
#63
Jwong684
closed
1 month ago
12
[Feature] how to handle updated output from different technologies.
#62
cstrlln
closed
1 month ago
5
[help wanted] Other segmentation options
#61
cstrlln
opened
1 month ago
4
Dev
#60
quentinblampey
closed
2 months ago
0
[Feature] Cellpose - artificially define an area of cytoplasm
#59
mariavigovaldoleiros
opened
2 months ago
1
[Feature] Use .CZI data in SOPA
#58
mariavigovaldoleiros
closed
2 weeks ago
3
Add patch embeddings with overlaps
#57
stergioc
closed
2 months ago
1
overlay segmentation #55
#56
quentinblampey
closed
2 months ago
0
Overlay custom segmentation using cell segmentation resolver
#55
EST09
closed
2 weeks ago
13
use double quotes in cli #49
#54
quentinblampey
closed
2 months ago
0
pin python 3.11 version in ci
#53
quentinblampey
closed
2 months ago
0
Dev
#52
quentinblampey
closed
2 months ago
0
Adds openslide backend
#51
stergioc
closed
2 months ago
1
Dev
#50
quentinblampey
closed
2 months ago
0
Vizgen-merscope
#49
HSvitina
closed
2 weeks ago
10
Questions about Spatial Statistics Analysis
#48
wikk-chy
closed
2 months ago
4
cell id corresponds
#47
Chuang1118
closed
2 months ago
6
support multi-tables
#46
quentinblampey
closed
2 months ago
0
hotfix v1.0.8
#45
quentinblampey
closed
2 months ago
0
upstream analysis
#44
rocketeer1998
closed
2 months ago
6
RuntimeError in rule patchify_cellpose: add_image(), add_labels(), add_points() and add_shapes()
#43
suhridbuddha
closed
2 months ago
6
ERROR in Patch_segmentation_baysor: Unable to find compatible target in cached code image. [Bug]
#42
jmchan88
closed
2 months ago
18
[Bug] Baysor fails when too few transcripts
#41
quentinblampey
closed
2 months ago
1
Merge v1.0.7
#40
quentinblampey
closed
3 months ago
0
pip install
#39
HSvitina
closed
3 months ago
2
Where is the tuto.zarr from the tuto.zarr?
#38
suhridbuddha
closed
1 month ago
4
ImportError: cannot import name '_get_unique_label_values_as_index' from 'spatialdata._core.query.relational_query'
#37
suhridbuddha
closed
2 months ago
4
CLI patching and cellpose segmentation + GPU
#35
andrea-de-micheli
closed
1 month ago
16
Dev
#34
quentinblampey
closed
3 months ago
0
Dev
#33
quentinblampey
closed
3 months ago
0
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