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Fixes - #216

Merged

dariarom94 merged 101 commits into

mainfrom

fixes

Aug 6, 2026

Merged

Fixes#216
dariarom94 merged 101 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)
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  committed
  82add80
- duplicates when FOV stiching cleaned up
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  committed
  53e1728
Commits on Jul 20, 2026
- chunks issue atera
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  committed
  1186b7a
- segger update image
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  committed
  18644d7
- claude fix for segger
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  committed
  ecb302d
- Merge branch 'main' into fixes
  dariarom94
  authored
  7d66898
- atera version fix
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  committed
  d400ebe
- wf for the custom rnaseq scripts
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  committed
  64d7b4e
- adjust the loader image name
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  committed
  3edfbf1
- adjust the memory
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  committed
  cbd2f12
- troubleshootig edges
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  committed
  184260e
- Merge branch 'main' into fixes
  dariarom94
  authored
  9fa9a33
Commits on Jul 21, 2026
- segger update
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  committed
  36631c4
- cell type label correction
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  committed
  0626127
- fix boundaries
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  committed
  3186435
- Merge branch 'main' into fixes
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  authored
  d8a7d93
- OOM fixes
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  committed
  3505718
- fix code
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  committed
  d6e110a
- RCTD
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  committed
  4660f26
- segger to RAPIDS
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  committed
  5abd651
- Merge branch 'main' into fixes
  dariarom94
  authored
  fe2e90a
Commits on Jul 22, 2026
- fix rctd
  dariarom94
  committed
  0b23474
- segger debug (torchvision)
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  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
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  committed
  123e112
- add fastreseg test
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  committed
  7549589
- Merge branch 'main' into fixes
  dariarom94
  authored
  9fa9604
- optimized fastreseg build
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  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)
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  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
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  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
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  committed
  9f71692
- Merge branch 'main' into fixes
  dariarom94
  authored
  d795f33
- param sweep
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  committed
  fefaadc
- add params to segmentation
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  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
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  committed
  3449bd0
- Merge branch 'main' into fixes
  dariarom94
  authored
  331d219
- adjust labels
  dariarom94
  committed
  5961d0a
Commits on Jul 31, 2026
- bruker nsclc
  dariarom94
  committed
  857e16a
- adjust bruker nsclc loader
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  committed
  54f023e
- setup
  dariarom94
  committed
  6e8b9ea
- Merge branch 'main' into fixes
  dariarom94
  authored
  4eec493
- method correction
  dariarom94
  committed
  44ad7af
- Merge branch 'main' into fixes
  dariarom94
  authored
  b351148
Commits on Aug 1, 2026
- pin anndata
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  committed
  2b8177c
- mirror nsclc
  dariarom94
  committed
  6c16707
Commits on Aug 2, 2026
- sync the vizgen files
  dariarom94
  committed
  5618fb8
- adjust mem for allen brain
  dariarom94
  committed
  b68c100
- claude notes
  dariarom94
  committed
  98dbc69
- claude notes
  dariarom94
  committed
  fa23294
- fix mirror script
  dariarom94
  committed
  ac9492c
- Merge branch 'main' into fixes
  dariarom94
  authored
  26d292e
Commits on Aug 3, 2026
- adapt fastreseg requirements
  dariarom94
  committed
  1ee371a
- merscope kuppe script update
  dariarom94
  committed
  c53016a
- fix nsclc loader
  dariarom94
  committed
  d479db6
Commits on Aug 4, 2026
- adjust mem for new test resources
  dariarom94
  committed
  6c54220
- adjust the nsclc loader for test resources
  dariarom94
  committed
  9494fc5
- change processor to avoid spatialdata 0.8.0 bug
  dariarom94
  committed
  a459afc
- pin spatialdata version
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  committed
  8f7b0c1
Commits on Aug 5, 2026
- memory fix
  dariarom94
  committed
  f18296b
- Merge branch 'main' into fixes
  dariarom94
  authored
  fc96dcb
- subsampling code
  dariarom94
  committed
  e75042f
- remove unexisting dataset
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  committed
  594bb25
- fix data extraction bag
  dariarom94
  committed
  90207aa
- transcript assignment edits
  dariarom94
  committed
  a94ec38
- segger: simplify transcript-assignment OOB handling to an edge clamp
  
  dariarom94
  and
  claude
  committed
  905b166
- modify proseg (param sweep)
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  committed
  b368d5e
Commits on Aug 6, 2026
- add scale0
  dariarom94
  committed
  0f57e2f
- Merge branch 'main' into fixes
  dariarom94
  authored
  5f09575
- fix code bug
  dariarom94
  committed
  c64f7d2
- expand test dataset space
  dariarom94
  committed
  7317d57
- Merge branch 'main' into fixes
  dariarom94
  authored
  fe3ad75
- fix stardist params
  dariarom94
  committed
  a0a3d43
- process_dataset: opt-in tissue-centered crop (fixes ABCA whole-brain MERFISH)
  
  dariarom94
  and
  claude
  committed
  6669752
- memory adjust
  dariarom94
  committed
  cc07559
- stardist tiling error
  dariarom94
  committed
  fcda921
- Merge branch 'main' into fixes
  dariarom94
  authored
  f26d173
- fix labels
  dariarom94
  committed
  4af3df3

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

Commits on Jul 31, 2026

Commits on Aug 1, 2026

Commits on Aug 2, 2026

Commits on Aug 3, 2026

Commits on Aug 4, 2026

Commits on Aug 5, 2026

Commits on Aug 6, 2026