Feature/ml stain normalization#1

Draft

LAdam-ix wants to merge 80 commits intomainfrom

feature/ml-stain-normalization

Commits on Nov 22, 2023

feat: core structure
matejpekar
committed

Commits on Nov 30, 2023

Commits on Dec 4, 2023

feat: syncing pipeline + google code styles
matejpekar
committed

Commits on Dec 6, 2023

Commits on Dec 21, 2023

Commits on Dec 22, 2023

Commits on Dec 23, 2023

feat: test coverage
matejpekar
committed

Commits on Dec 25, 2023

feat: allow installing gitlab dependecies in CI/CD
matejpekar
committed

Commits on Jan 6, 2024

chore: ignore mlflow_store
matejpekar
committed

Commits on May 24, 2024

chore: new libary template
matejpekar
committed

Commits on Aug 17, 2024

feat: routines for separating and combining stain channels, and stain estimation

TomasBalak
authored and
matejpekar
committed

Commits on Aug 27, 2024

Commits on Sep 9, 2024

fix: py.typed marker file
matejpekar
committed

Commits on Feb 28, 2025

feat: light H&DAB protocol, color conversion fixes, modify and reconstruct

TomasBalak
authored and
matejpekar
committed

Commits on Mar 4, 2025

feat: ml init
LAdam-ix
committed

Commits on Mar 7, 2025

fix: transformations inputs
Adam Lopatka
committed
chore: added data link
Adam Lopatka
committed
fix: resolve issues before job run
Adam Lopatka
committed
chore: job config
Adam Lopatka
committed
fix: job run parametrs
Adam Lopatka
committed
fix: lower batch size
Adam Lopatka
committed
fix: lower workers
Adam Lopatka
committed
fix: ensure float32 tensors
Adam Lopatka
committed
fix: missing ()
Adam Lopatka
committed
fix: decode_head settings
Adam Lopatka
committed
chore: config change
Adam Lopatka
committed

Commits on Mar 9, 2025

fix: job settign optimalization
Adam Lopatka
committed

Commits on Mar 13, 2025

fix: image normalization
Adam Lopatka
committed

Commits on Mar 23, 2025

feat: tiles export
Adam Lopatka
committed
feat: update loss function
Adam Lopatka
committed

Commits on Mar 27, 2025

fix: p=1
Adam Lopatka
committed

Commits on Mar 28, 2025

fix: more frequent validation
Adam Lopatka
committed

Commits on Mar 29, 2025

fix: val logging
Adam Lopatka
committed
fix: val logging
Adam Lopatka
committed
fix: repair loss function
Adam Lopatka
committed
fix: revert val logging
Adam Lopatka
committed
fix: optimalise train data load
Adam Lopatka
committed
fix: update val frequency
Adam Lopatka
committed

Commits on Apr 18, 2025

feat: change to full unet
Adam Lopatka
committed
chore: update job setup
Adam Lopatka
committed
chore: update job setup
Adam Lopatka
committed

Commits on May 16, 2025

chore: code cleanup
Adam Lopatka
committed
chore: formating fix
Adam Lopatka
committed
chore: formating fix
Adam Lopatka
committed
chore: formating fix
Adam Lopatka
committed

Commits on May 18, 2025

chore: remove kubejobs
Adam Lopatka
committed

Commits on May 19, 2025

chore: naming fix
Adam Lopatka
committed
chore: add comments and fix formating
LAdam-ix
committed
feat: added demo
LAdam-ix
committed
fix: formating
LAdam-ix
committed
fix: arguments
Adam Lopatka
committed

Commits on Nov 29, 2025

feat: add brightness loss and analysis
Adam Lopatka
committed
feat: update dataset slide paths
Adam Lopatka
committed

Commits on Dec 5, 2025

fix: adjust hyperparameters
LAdam-ix
authored

Commits on Dec 7, 2025

chore: add checkpoint path
LAdam-ix
authored

Commits on Dec 8, 2025

Commits on Dec 12, 2025

chore: update checkpoint
Adam Lopatka
committed

Commits on Mar 4, 2026

feat: update analysis methods and WSI assembly
LAdam-ix
committed

Commits on Mar 5, 2026

chore: merge main history
LAdam-ix
committed