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Fixes - #198

Merged

dariarom94 merged 61 commits into

mainfrom

fixes

Jul 30, 2026

Merged

Fixes#198
dariarom94 merged 61 commits into
mainfrom
fixes

Commits on Jul 19, 2026
- Register cellposev4 in benchmark run scripts
  
  dariarom94
  and
  claude
  committed
  f80b261
- fix anndata version mismatch with txsim
  dariarom94
  committed
  1a2fa09
- add segger to workflow (test)
  dariarom94
  committed
  82add80
- duplicates when FOV stiching cleaned up
  dariarom94
  committed
  53e1728
Commits on Jul 20, 2026
- chunks issue atera
  dariarom94
  committed
  1186b7a
- segger update image
  dariarom94
  committed
  18644d7
- claude fix for segger
  dariarom94
  committed
  ecb302d
- Merge branch 'main' into fixes
  dariarom94
  authored
  7d66898
- atera version fix
  dariarom94
  committed
  d400ebe
- wf for the custom rnaseq scripts
  dariarom94
  committed
  64d7b4e
- adjust the loader image name
  dariarom94
  committed
  3edfbf1
- adjust the memory
  dariarom94
  committed
  cbd2f12
- troubleshootig edges
  dariarom94
  committed
  184260e
- Merge branch 'main' into fixes
  dariarom94
  authored
  9fa9a33
Commits on Jul 21, 2026
- segger update
  dariarom94
  committed
  36631c4
- cell type label correction
  dariarom94
  committed
  0626127
- fix boundaries
  dariarom94
  committed
  3186435
- Merge branch 'main' into fixes
  dariarom94
  authored
  d8a7d93
- OOM fixes
  dariarom94
  committed
  3505718
- fix code
  dariarom94
  committed
  d6e110a
- RCTD
  dariarom94
  committed
  4660f26
- segger to RAPIDS
  dariarom94
  committed
  5abd651
- Merge branch 'main' into fixes
  dariarom94
  authored
  fe2e90a
Commits on Jul 22, 2026
- fix rctd
  dariarom94
  committed
  0b23474
- segger debug (torchvision)
  dariarom94
  committed
  196ff1f
- Merge branch 'main' into fixes
  dariarom94
  authored
  4be7bd4
- save the xenium version
  dariarom94
  committed
  b8d3d7b
- add atera to datasets
  dariarom94
  committed
  202ac49
- Add gene efficiency correction as a separate pipeline stage (#183)
  
  dariarom94
  and
  claude
  authored
  14be8d0
- moscot to pca and segger troubleshooting
  dariarom94
  committed
  0cf0243
Commits on Jul 23, 2026
- added fastreseg
  dariarom94
  committed
  d7afb84
- segger bug new fix
  dariarom94
  committed
  f87a1d9
- fastreseg to workflow
  dariarom94
  committed
  123e112
- add fastreseg test
  dariarom94
  committed
  7549589
- Merge branch 'main' into fixes
  dariarom94
  authored
  9fa9604
- optimized fastreseg build
  dariarom94
  committed
  ff04467
- Merge branch 'main' into fixes
  dariarom94
  authored
  7ffc514
Commits on Jul 24, 2026
- add s3 paths
  dariarom94
  committed
  a7404d8
- troubleshoot comseg/segger
  dariarom94
  committed
  19e5f83
Commits on Jul 25, 2026
- segger update
  dariarom94
  committed
  aaca151
- data loader bug
  dariarom94
  committed
  c9bdb91
- Merge branch 'main' into fixes
  dariarom94
  authored
  1df9834
Commits on Jul 26, 2026
- rctd adjustment (raw counts)
  dariarom94
  committed
  4467d32
- fix segger and comseg
  dariarom94
  committed
  58912e4
- optimize cosmx
  dariarom94
  committed
  0a5aa99
- Merge branch 'main' into fixes
  dariarom94
  authored
  298e666
- parameter test for cellpose4
  dariarom94
  committed
  c921937
- add atera
  dariarom94
  committed
  57c2d79
Commits on Jul 27, 2026
- add a test in pciseq and dynamic memory for bruker
  dariarom94
  committed
  cf67e09
Commits on Jul 28, 2026
- add test to vizgen data
  dariarom94
  committed
  9f71692
- Merge branch 'main' into fixes
  dariarom94
  authored
  d795f33
- param sweep
  dariarom94
  committed
  fefaadc
- add params to segmentation
  dariarom94
  committed
  4dc08d3
Commits on Jul 29, 2026
- adjust segger mem
  dariarom94
  committed
  e9505f1
- update fastreseg to tacco
  dariarom94
  committed
  3a155be
Commits on Jul 30, 2026
- Add annotation + expression-correction parameter sweeps (rctd, ssam, tangram, resolvi)
  
  dariarom94
  and
  claude
  committed
  acdd6c7
- Add moscot + split parameter sweeps (annotation, expression correction)
  
  dariarom94
  and
  claude
  committed
  fa462b8
- singler: read par['celltype_key'] instead of hardcoding "cell_type"
  
  dariarom94
  and
  claude
  committed
  fd37aee
- fastreseg
  dariarom94
  committed
  3449bd0
- Merge branch 'main' into fixes
  dariarom94
  authored
  331d219
- adjust labels
  dariarom94
  committed
  5961d0a

Commits

Commits on Jul 19, 2026

Commits on Jul 20, 2026

Commits on Jul 21, 2026

Commits on Jul 22, 2026

Commits on Jul 23, 2026

Commits on Jul 24, 2026

Commits on Jul 25, 2026

Commits on Jul 26, 2026

Commits on Jul 27, 2026

Commits on Jul 28, 2026

Commits on Jul 29, 2026

Commits on Jul 30, 2026