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Revision - #3

Merged

marta-seq merged 31 commits into

mainfrom

revision

Apr 12, 2026

Merged

Revision#3
marta-seq merged 31 commits into
mainfrom
revision

Commits on Jan 25, 2026
- add notebook using PENGUIN to preprocess IMC and IF
  marta-seq
  committed
  6876b91
- add notebook that explores Cosmx agridgene vs reference. start with Xenium
  marta-seq
  committed
  1031b4a
Commits on Jan 26, 2026
- update notebook that explores agridgene vs reference. Xenium
  marta-seq
  committed
  4a333ad
- update notebook that explores agridgene vs reference. Xenium
  marta-seq
  committed
  1e87b01
Commits on Feb 4, 2026
- update on quantitative xenium
  marta-seq
  committed
  082a72b
Commits on Feb 6, 2026
- add quantitative validation for cell validation
  marta-seq
  committed
  ac3d6ae
Commits on Feb 7, 2026
- add quantitative validation for cell validatio changesn
  marta-seq
  committed
  3fd7adb
Commits on Feb 8, 2026
- add runtime analysis
  marta-seq
  committed
  e44e8af
- WIP: current work before branch restructure
  marta-seq
  committed
  2835f10
- clean and improve runtime with clear subprocesses benchmarks
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  committed
  63600c4
- fix on binsom logger
  marta-seq
  committed
  e1ed564
Commits on Feb 9, 2026
- refactor of quant analysis. fix cosmx and IF
  marta-seq
  committed
  2cafeef
Commits on Feb 10, 2026
- update on validation code for Xeniuma nd CosMx
  marta-seq
  committed
  f9bdc49
Commits on Feb 12, 2026
- update notebook xenium quantitative
  marta-seq
  committed
  4c01f3b
- add function on validation
  marta-seq
  committed
  63aded9
Commits on Feb 13, 2026
- fix the cell phenotyping overlap with gridgene masks
  marta-seq
  committed
  144dc3d
Commits on Feb 18, 2026
- add plot on Xenium part
  marta-seq
  committed
  656da38
Commits on Feb 23, 2026
- fix plots runtime_performance and clean code
  marta-seq
  committed
  eca3435
- include instalation guidelines
  marta-seq
  committed
  4581012
Commits on Mar 11, 2026
- orthogonal validation cell segmentation
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  committed
  88c888c
Commits on Mar 14, 2026
- orthogonal validation cell segmentation imporvment
  marta-seq
  committed
  cb5dcde
- validation against manual masks. deletion of redundant notebooks
  marta-seq
  committed
  85b628a
- remove tracked folders
  marta-seq
  committed
  cdfee02
- add new notebook on gd xenium validation
  marta-seq
  committed
  e552491
Commits on Apr 6, 2026
- add new notebook on gd xenium validation - small fixes
  marta-seq
  committed
  0677448
Commits on Apr 11, 2026
- clean and improve images orthogonal ipynb
  marta-seq
  committed
  a85010f
Commits on Apr 12, 2026
- clean and improve images orthogonal ipynb
  marta-seq
  committed
  65a69c2
- clean and improve images manual annotation ipynb
  marta-seq
  committed
  f60ed67
- remove figures from tracking, add to gitignore
  marta-seq
  committed
  b482bdb
- remove to_delete folder from tracking
  marta-seq
  committed
  355ae3f
- remove benchmark_plots from tracking
  marta-seq
  committed
  aedde91

Commits

Commits on Jan 25, 2026

Commits on Jan 26, 2026

Commits on Feb 4, 2026

Commits on Feb 6, 2026

Commits on Feb 7, 2026

Commits on Feb 8, 2026

Commits on Feb 9, 2026

Commits on Feb 10, 2026

Commits on Feb 12, 2026

Commits on Feb 13, 2026

Commits on Feb 18, 2026

Commits on Feb 23, 2026

Commits on Mar 11, 2026

Commits on Mar 14, 2026

Commits on Apr 6, 2026

Commits on Apr 11, 2026

Commits on Apr 12, 2026