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29 Open 87 Closed
29 Open 87 Closed
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Issues list

[help wanted] FileNotFoundError: [Errno 2] No such file or directory for --sopa resolve baysor
#161 opened Dec 3, 2024 by KunHHE
3
[Feature] Multiple run of Cellpose/Baysor
#154 opened Nov 19, 2024 by lguerard
2
Issue resolving conflicts with resolve() for Baysor segmentation
#152 opened Nov 8, 2024 by NJNataren
4
[Feature] Bypass Baysor patches where no cells
#150 opened Nov 4, 2024 by lguerard
4
Obtaining transcript confidence and assignment_confidence from baysor segmentation
#149 opened Nov 4, 2024 by pngai1
2
How to analyze one tissue section data separately from one capture area which include two tissue sections for Xenium 5k ?
#148 opened Nov 3, 2024 by lidd77
1
Min & Max aggregation methods enhancement New feature or request
#147 opened Nov 1, 2024 by dancelestini
4
[Bug] Parallelization backend issues with dask
#145 opened Oct 30, 2024 by quentinblampey
[Bug] Xenium Prime - empty codewords included in the SOPA output enhancement New feature or request
#144 opened Oct 25, 2024 by wlason
1
[Bug] Mistake in slurm config yaml
#141 opened Oct 22, 2024 by wlason
1
[Feature] Allow setting of run_name in sopa explorer write enhancement New feature or request
#139 opened Oct 16, 2024 by pakiessling
2
Unable to read a whole slide image into sopa
#137 opened Oct 8, 2024 by asmitaL99
8
[Bug] Polygon resolution after cellpose leads to overlapping and misshapen cells
#136 opened Oct 4, 2024 by pakiessling
1
[Feature] Assigning transcript (points) to cells
#132 opened Sep 29, 2024 by pakiessling
8
[Feature] Cell Boundary Expansion in DAPI Stained Fluorescence Images enhancement New feature or request
#130 opened Sep 26, 2024 by guoyang-github
4
[Bug] Isse with running Baysor segmentation on some but not all patches
#123 opened Sep 12, 2024 by marsdenl
20
Handling pseudo 3D information
#122 opened Sep 9, 2024 by Marius1311
3
[Feature & Bug] Xenium explorer displaying both Cellpose and Baysor boundaries
#120 opened Sep 7, 2024 by lguerard
6
[Bug]"Could not find element with name ['cell_circles']"
#117 opened Sep 2, 2024 by Yifan-debug
7
[Feature] General reader for non-commercial datasets
#116 opened Sep 2, 2024 by lopollar
3
sopa.segmentation.transcripts.resolve for Baysor segmentation fails
#115 opened Aug 30, 2024 by Marius1311
5
saving masks to png
#112 opened Aug 23, 2024 by sunshx-bioinfo
9
Scaling sopa to run many images
#103 opened Aug 5, 2024 by josenimo
5
Incompatible coordinate transformation with cellpose segmentation result
#96 opened Jul 23, 2024 by mamyAndrianteranagna
14
snakemake executes wrong rule
#84 opened Jul 3, 2024 by xiao233333
1
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