1 Pull request opened by 1 person

• 166 using sopa as module in workflow leads to name error the name paths is unknown in this context

  #167 opened Dec 20, 2024

9 Issues closed by 5 people

• reading .hdf5 file in sopa?

  #163 closed Dec 27, 2024

• AnnData h5ad from Scimap output is compatible with the Sopa package for Spatial statistics?

  #170 closed Dec 26, 2024

• [Bug]SpatialData.__init__() got an unexpected keyword argument 'attrs'

  #168 closed Dec 21, 2024

• [Bug] ImportError: cannot import name 'HybridMappingProxy

  #164 closed Dec 20, 2024

• Writing CosMX segmentation+transcripts to Xenium explorer

  #162 closed Dec 9, 2024

• Sopa read: Could not infer `dataset_id`

  #146 closed Dec 6, 2024

• running error on MissingInputException in rule resolve_cellpose for merscope data

  #156 closed Dec 3, 2024

• Patch # has < 4000 transcripts. Segmentation will not be run?

  #157 closed Dec 3, 2024

• patch running for Baysor in CLI

  #160 closed Dec 3, 2024

7 Issues opened by 4 people

• [Help wanted] --save-h5ad but missed transcript counts

  #173 opened Dec 28, 2024

• multiple samples for spatial analysis using sopa

  #172 opened Dec 27, 2024

• "niches" from demo data in Spatial statistics section

  #171 opened Dec 25, 2024

• [Bug] Sopa2 error when no cells are found in FOV

  #169 opened Dec 22, 2024

• Using sopa as module in workflow leads to NameError: The name 'paths' is unknown in this context

  #166 opened Dec 20, 2024

• [Feature] Sopa2 with BIDcell/segger

  #165 opened Dec 18, 2024

• [help wanted] FileNotFoundError: [Errno 2] No such file or directory for --sopa resolve baysor

  #161 opened Dec 3, 2024

6 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• [Feature & Bug] Xenium explorer displaying both Cellpose and Baysor boundaries

  #120 commented on Nov 30, 2024 • 0 new comments

• Unable to read a whole slide image into sopa

  #137 commented on Dec 6, 2024 • 0 new comments

• Handling pseudo 3D information

  #122 commented on Dec 9, 2024 • 0 new comments

• saving masks to png

  #112 commented on Dec 24, 2024 • 0 new comments

• data reproduce on annotation for sopa paper

  #158 commented on Dec 28, 2024 • 0 new comments

• [Feature] Multiple run of Cellpose/Baysor

  #154 commented on Dec 28, 2024 • 0 new comments