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24 Open 109 Closed
24 Open 109 Closed
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Issues list

[Feature] Allow two separate categories of shapes to be written to Xenium Explorer
#182 opened Jan 21, 2025 by pakiessling
7
[Feature] Clarify how to get the CosMX input
#180 opened Jan 21, 2025 by quentinblampey
ValueError: Invalid dtype int64 for prior cell ids. Must be int or string.
#179 opened Jan 21, 2025 by marsdenl
2
[Bug] sopa write explorer fails after H&E image is added
#176 opened Jan 10, 2025 by jpark27
1
[Help wanted] --save-h5ad but missed transcript counts
#173 opened Dec 28, 2024 by KunHHE
2
[Feature] Sopa2 with BIDcell/segger
#165 opened Dec 18, 2024 by jpark27
4
reading .hdf5 file in sopa?
#163 opened Dec 13, 2024 by KunHHE
5
[Feature] Multiple run of Cellpose/Baysor
#154 opened Nov 19, 2024 by lguerard
6
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
[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] Polygon resolution after cellpose leads to overlapping and misshapen cells
#136 opened Oct 4, 2024 by pakiessling
1
[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
4
[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
saving masks to png
#112 opened Aug 23, 2024 by sunshx-bioinfo
12
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
Immunofluorescence Image Segmentation
#78 opened Jun 6, 2024 by suhridbuddha
1
Add nextflow pipeline enhancement New feature or request help wanted Extra attention is needed
#7 opened Dec 1, 2023 by quentinblampey
2
ProTip! Exclude everything labeled bug with -label:bug.