From 6e1d4b9ac92f9266953501620d265f0d4cfabcaf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 15:46:20 +0000
Subject: [PATCH 01/12] chore: replace pdm with uv

---
 .gitignore              |    1 +
 .pre-commit-config.yaml |   23 -
 pdm.lock                | 2114 -----------------------------------
 pyproject.toml          |   46 +-
 uv.lock                 | 2316 +++++++++++++++++++++++++++++++++++++++
 5 files changed, 2337 insertions(+), 2163 deletions(-)
 delete mode 100644 .pre-commit-config.yaml
 delete mode 100644 pdm.lock
 create mode 100644 uv.lock

diff --git a/.gitignore b/.gitignore
index 1c12553..9075af1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -180,3 +180,4 @@ lightning_logs/
 
 # Project
 /data
+playground.ipynb
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
deleted file mode 100644
index ce018d9..0000000
--- a/.pre-commit-config.yaml
+++ /dev/null
@@ -1,23 +0,0 @@
-# See https://pre-commit.com for more information
-# See https://pre-commit.com/hooks.html for more hooks
-repos:
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
-    hooks:
-      - id: check-yaml
-        args: [--unsafe]
-
-  - repo: https://github.com/commitizen-tools/commitizen
-    rev: v3.29.0
-    hooks:
-      - id: commitizen
-
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
-    hooks:
-      # Run the linter.
-      - id: ruff
-        entry: pdm lint --force-exclude
-      # Run the formatter.
-      - id: ruff-format
-        entry: pdm format --force-exclude
diff --git a/pdm.lock b/pdm.lock
deleted file mode 100644
index 6faa76e..0000000
--- a/pdm.lock
+++ /dev/null
@@ -1,2114 +0,0 @@
-# This file is @generated by PDM.
-# It is not intended for manual editing.
-
-[metadata]
-groups = ["default", "dev"]
-strategy = ["inherit_metadata"]
-lock_version = "4.5.0"
-content_hash = "sha256:212d57f14fc7d3add49c7d17f3ab69baa2c5b3809a0a5e0cf2fb88dea5eed593"
-
-[[metadata.targets]]
-requires_python = ">=3.11"
-
-[[package]]
-name = "aiohappyeyeballs"
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-requires_python = ">=3.8"
-summary = "Happy Eyeballs for asyncio"
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-
-[[package]]
-name = "zipp"
-version = "3.20.1"
-requires_python = ">=3.8"
-summary = "Backport of pathlib-compatible object wrapper for zip files"
-groups = ["default"]
-files = [
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diff --git a/pyproject.toml b/pyproject.toml
index 0c198ab..39445e2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,34 +1,28 @@
 [project]
-name = "project-name"
+name = "ulcerative-colitis"
 version = "0.1.0"
-authors = []
-requires-python = ">=3.11"
+authors = [{name = "Adam Kukučka", email = "adam.kukucka@mail.muni.cz"}]
+requires-python = ">=3.12,<3.13"
 readme = "README.md"
 license = { file = "LICENSE" }
 dependencies = [
-    "torch>=2.4.0",
-    "lightning>=2.4.0",
-    "torchmetrics>=1.4.1",
-    "rationai-mlkit @ git+https://gitlab.ics.muni.cz/rationai/digital-pathology/libraries/mlkit.git",
+    "aiohttp>=3.13.2",
+    "lightning>=2.5.6",
+    "mlflow<3.0.0",
+    "omegaconf>=2.3.0",
+    "openpyxl>=3.1.5",
+    "pandas>=2.3.3",
+    "pyvips<3.1",
+    "rationai-mlkit",
+    "ray>=2.52.1",
+    "torch>=2.9.0",
+    "torchmetrics>=1.8.2",
 ]
 
-[tool.pdm.dev-dependencies]
-dev = ["mypy", "pre-commit", "ruff"]
+[dependency-groups]
+dev = ["mypy", "ruff", "ipykernel"]
+run = ["rationai-kube-jobs"]
 
-[tool.pdm.scripts]
-train = "python -m project_name mode=fit"
-validate = "python -m project_name mode=validate"
-test = "python -m project_name mode=test"
-predict = "python -m project_name mode=predict"
-l = { composite = ["lint", "format", "mypy"] }
-lint = "ruff check --fix"
-format = "ruff format"
-mypy = "mypy ."
-post_install = { composite = [
-    "pre-commit autoupdate",
-    "pre-commit install",
-    "pre-commit install --hook-type commit-msg",
-] }
-
-[tool.pdm]
-distribution = false
+[tool.uv.sources]
+rationai-mlkit = { git = "https://gitlab.ics.muni.cz/rationai/digital-pathology/libraries/mlkit.git" }
+rationai-kube-jobs = { git = "ssh://git@gitlab.ics.muni.cz/rationai/infrastructure/kube-jobs" }
diff --git a/uv.lock b/uv.lock
new file mode 100644
index 0000000..baa2405
--- /dev/null
+++ b/uv.lock
@@ -0,0 +1,2316 @@
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+revision = 3
+requires-python = "==3.12.*"
+resolution-markers = [
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From d7a1ef31b9f4a65266522aff0e2e938606948581 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 15:47:07 +0000
Subject: [PATCH 02/12] feat: configs

---
 configs/data/raw/ftn.yaml       |  8 ++++++++
 configs/data/raw/ikem.yaml      |  9 +++++++++
 configs/data/raw/knl_patos.yaml | 10 ++++++++++
 configs/default.yaml            | 15 +--------------
 configs/preprocessing.yaml      |  9 +++++++++
 5 files changed, 37 insertions(+), 14 deletions(-)
 create mode 100644 configs/data/raw/ftn.yaml
 create mode 100644 configs/data/raw/ikem.yaml
 create mode 100644 configs/data/raw/knl_patos.yaml
 create mode 100644 configs/preprocessing.yaml

diff --git a/configs/data/raw/ftn.yaml b/configs/data/raw/ftn.yaml
new file mode 100644
index 0000000..c70f757
--- /dev/null
+++ b/configs/data/raw/ftn.yaml
@@ -0,0 +1,8 @@
+# @package _global_
+
+dataset:
+  institution: ftn
+  folder: /mnt/data/FTN/colon/IBD_AI
+  labels:
+    - IBD_AI_FTN.xlsx
+    - IBD_AI_FTN_doplnek.xlsx
\ No newline at end of file
diff --git a/configs/data/raw/ikem.yaml b/configs/data/raw/ikem.yaml
new file mode 100644
index 0000000..5cc8ba4
--- /dev/null
+++ b/configs/data/raw/ikem.yaml
@@ -0,0 +1,9 @@
+# @package _global_
+
+dataset:
+  institution: ikem
+  folder: /mnt/data/IKEM/colon/IBD_AI/20x
+  labels:
+    - Fab_IBD_AI_12_2024.csv
+    - IBD_AI_2.xlsx
+    - missing.xlsx
\ No newline at end of file
diff --git a/configs/data/raw/knl_patos.yaml b/configs/data/raw/knl_patos.yaml
new file mode 100644
index 0000000..326cbbd
--- /dev/null
+++ b/configs/data/raw/knl_patos.yaml
@@ -0,0 +1,10 @@
+# @package _global_
+
+dataset:
+  institution: knl_patos
+  folder: /mnt/data/KNL_PATOS/colon/IBD_AI
+  labels:
+    - IBD_AI_Liberec.xlsx
+    - IBD_AI_Liberec_02.xlsx
+    - IBD_AI_Liberec_10_2025.xlsx
+    - IBD_AI_Liberec_28_10_2025.xlsx
\ No newline at end of file
diff --git a/configs/default.yaml b/configs/default.yaml
index 20eabdd..94c880e 100644
--- a/configs/default.yaml
+++ b/configs/default.yaml
@@ -3,18 +3,5 @@ defaults:
   - logger: mlflow
   - _self_
 
-seed: ${random_seed:}
-mode: ???
-checkpoint: null
-
-trainer: {}
-
-data: {}
-
-model: {}
-
 metadata:
-  experiment_name: ???
-  run_name: ???
-  description: ???
-  hyperparams: {}
+  experiment_name: Ulcerative Colitis
diff --git a/configs/preprocessing.yaml b/configs/preprocessing.yaml
new file mode 100644
index 0000000..6af2711
--- /dev/null
+++ b/configs/preprocessing.yaml
@@ -0,0 +1,9 @@
+# @package _global_
+
+defaults:
+  - base
+  - _self_
+
+dataset: ???
+    
+project_dir: /mnt/projects/inflammatory_bowel_dissease/ulcerative_colitis

From 34abac4e1a1153b4fe08c9fac62d9ca589f53c99 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 15:47:19 +0000
Subject: [PATCH 03/12] feat: dataset creation

---
 configs/preprocessing/create_dataset.yaml |   5 +
 preprocessing/create_dataset.py           | 134 ++++++++++++++++++++++
 2 files changed, 139 insertions(+)
 create mode 100644 configs/preprocessing/create_dataset.yaml
 create mode 100644 preprocessing/create_dataset.py

diff --git a/configs/preprocessing/create_dataset.yaml b/configs/preprocessing/create_dataset.yaml
new file mode 100644
index 0000000..7fbd40d
--- /dev/null
+++ b/configs/preprocessing/create_dataset.yaml
@@ -0,0 +1,5 @@
+# @package _global_
+
+metadata:
+  run_name: "📂 Dataset Creation: {dataset.institution}"
+  description: "Create dataset for {dataset.institution} institution"
diff --git a/preprocessing/create_dataset.py b/preprocessing/create_dataset.py
new file mode 100644
index 0000000..d0286fb
--- /dev/null
+++ b/preprocessing/create_dataset.py
@@ -0,0 +1,134 @@
+import re
+import tempfile
+from pathlib import Path
+
+import hydra
+import pandas as pd
+from omegaconf import DictConfig
+from rationai.mlkit import autolog, with_cli_args
+from rationai.mlkit.lightning.loggers import MLFlowLogger
+
+
+REGEX = {
+    # [0-9]{1,5} - case ID (1 to 5 digits) (in year scope)
+    # _ - underscore separator
+    # 2[1-4] - year (2021 to 2024)
+    # _ - underscore separator
+    # HE - stain type
+    # (?:_0[1-6])? - optional underscore and slide number (01 to 06)
+    # .czi - file extension
+    "ikem": re.compile(r"^[0-9]{1,5}_2[1-4]_HE(?:_0[1-6])?\.czi"),
+    # [0-9]{1,6} - case ID (1 to 6 digits) (in year scope)
+    # _ - underscore separator
+    # 2[0-5] - year (2020 to 2025)
+    # .czi - file extension
+    "ftn": re.compile(r"[0-9]{1,6}_2[0-5]\.czi"),
+    # [0-9]{1,5} - case ID (1 to 5 digits) (in year scope)
+    # _ - underscore separator
+    # 25 - year 2025
+    # _ - underscore separator
+    # [A-F] - block identifier (A to F)
+    # _ - underscore separator
+    # HE - stain type
+    # (0[1-9]|1[0-2]) - slide number (01 to 12)
+    # .czi - file extension
+    "knl_patos": re.compile(r"[0-9]{1,5}_25_[A-F]_HE(0[1-9]|1[0-2])\.czi"),
+}
+
+
+def get_labels(folder_path: Path, labels: list[str]) -> pd.DataFrame:
+    dfs = []
+    for labels_file in labels:
+        labels_path = Path(folder_path) / labels_file
+
+        if labels_path.suffix == ".csv":
+            # One labels file is in CSV format
+            df = pd.read_csv(labels_path, index_col=0)
+        else:
+            df = pd.read_excel(labels_path, index_col=0)
+
+        df.columns = df.columns.str.lower()
+        dfs.append(df)
+
+    labels_df = pd.concat(dfs)
+    # id is in format [case_id]/YY (e.g., 01234/24 or 1234/24)
+    labels_df.index = labels_df.index.str.lstrip("0")
+    labels_df.index = labels_df.index.str.strip()
+    labels_df.index = labels_df.index.str.replace("/", "_", regex=False)
+
+    return labels_df
+
+
+def get_slides(folder_path: Path, institution: str) -> pd.DataFrame:
+    slides = []
+    for slide_path in folder_path.iterdir():
+        if not REGEX[institution].fullmatch(slide_path.name):
+            continue
+        case_id = "_".join(slide_path.stem.split("_")[:2])
+
+        slides.append(
+            {"slide_id": slide_path.stem, "case_id": case_id, "path": str(slide_path)}
+        )
+
+    slides_df = pd.DataFrame(slides).set_index("slide_id")
+    return slides_df
+
+
+def create_dataset(
+    folder: str, labels: list[str], institution: str
+) -> tuple[pd.DataFrame, list[str], list[str]]:
+    folder_path = Path(folder)
+    labels_df = get_labels(folder_path, labels)
+    slides_df = get_slides(folder_path, institution)
+
+    # IKEM has only case-level labels (FTN has one slide per case)
+    on = "case_id" if institution == "ikem" else "slide_id"
+    dataset_df = slides_df.join(labels_df, on=on, how="outer")
+
+    if institution == "ikem":
+        # IKEM has 'Lokalita' and 'Diagnóza' columns
+        # Slides inside ileum are not used
+        dataset_df = dataset_df[dataset_df["lokalita"] != "ileum"]
+        # Columns 'Lokalita' and 'Diagnóza' are no longer needed
+
+    missing_labels = dataset_df[dataset_df["nancy"].isna()].index.to_list()
+    missing_slides = dataset_df[dataset_df["path"].isna()][on].to_list()
+
+    dataset_df = dataset_df[["case_id", "path", "nancy"]]
+    dataset_df = dataset_df.dropna()
+
+    return dataset_df, missing_slides, missing_labels
+
+
+@with_cli_args(["+preprocessing=create_dataset"])
+@hydra.main(config_path="../configs", config_name="preprocessing", version_base=None)
+@autolog
+def main(config: DictConfig, logger: MLFlowLogger) -> None:
+    dataset, missing_slides, missing_labels = create_dataset(
+        config.dataset.folder, config.dataset.labels, config.dataset.institution
+    )
+
+    with tempfile.TemporaryDirectory() as tmpdir:
+        tmpdir_path = Path(tmpdir)
+
+        output_path = tmpdir_path / "dataset.csv"
+        dataset.to_csv(output_path, index=True)
+        logger.log_artifact(str(output_path))
+
+        if missing_slides:
+            missing_slides_path = tmpdir_path / "missing_slides.txt"
+            with open(missing_slides_path, "w") as f:
+                for slide in missing_slides:
+                    f.write(f"{slide}\n")
+            logger.log_artifact(str(missing_slides_path))
+
+        if missing_labels:
+            missing_labels_path = tmpdir_path / "missing_labels.txt"
+            with open(missing_labels_path, "w") as f:
+                for label in missing_labels:
+                    f.write(f"{label}\n")
+            logger.log_artifact(str(missing_labels_path))
+
+
+if __name__ == "__main__":
+    main()

From 80eca85d08f6a7935d786f3eb431594534907f25 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 15:57:44 +0000
Subject: [PATCH 04/12] fix: configs

---
 configs/{default.yaml => base.yaml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename configs/{default.yaml => base.yaml} (100%)

diff --git a/configs/default.yaml b/configs/base.yaml
similarity index 100%
rename from configs/default.yaml
rename to configs/base.yaml

From 97335eff0eb0ec44204f7b4ceeba0280207483d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 16:00:44 +0000
Subject: [PATCH 05/12] fix: configs

---
 configs/preprocessing/create_dataset.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/configs/preprocessing/create_dataset.yaml b/configs/preprocessing/create_dataset.yaml
index 7fbd40d..154709e 100644
--- a/configs/preprocessing/create_dataset.yaml
+++ b/configs/preprocessing/create_dataset.yaml
@@ -1,5 +1,5 @@
 # @package _global_
 
 metadata:
-  run_name: "📂 Dataset Creation: {dataset.institution}"
-  description: "Create dataset for {dataset.institution} institution"
+  run_name: "📂 Dataset Creation: ${dataset.institution}"
+  description: "Create dataset for ${dataset.institution} institution"

From 727c729db7aaf31944805fd4c533a7c9869aef0c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 16:00:54 +0000
Subject: [PATCH 06/12] feat: add scripts

---
 .mypy.ini                               |  3 ++-
 scripts/preprocessing/create_dataset.py | 20 ++++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)
 create mode 100644 scripts/preprocessing/create_dataset.py

diff --git a/.mypy.ini b/.mypy.ini
index 1c6f44e..abd4983 100644
--- a/.mypy.ini
+++ b/.mypy.ini
@@ -2,4 +2,5 @@
 strict = True
 ignore_missing_imports = True
 disallow_untyped_calls = False
-disable_error_code = no-any-return
\ No newline at end of file
+disable_error_code = no-any-return
+exclude = scripts
\ No newline at end of file
diff --git a/scripts/preprocessing/create_dataset.py b/scripts/preprocessing/create_dataset.py
new file mode 100644
index 0000000..6595cfa
--- /dev/null
+++ b/scripts/preprocessing/create_dataset.py
@@ -0,0 +1,20 @@
+from kube_jobs import storage, submit_job
+
+
+COHORT = "ikem"  # "ikem", "ftn", or "knl_patos"
+
+submit_job(
+    job_name=f"ulcerative-colitis-dataset-creation-{COHORT}",
+    username=...,
+    public=False,
+    cpu=2,
+    memory="4Gi",
+    script=[
+        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/ulcerative-colitis.git workdir",
+        "cd workdir",
+        "git checkout feature/dataset",
+        "uv sync --frozen",
+        f"uv run -m preprocessing.create_dataset +data=raw/{COHORT}",
+    ],
+    storage=[storage.secure.DATA],
+)

From fa9f5817065091c758376241fcdce81a21ae1880 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 16:06:50 +0000
Subject: [PATCH 07/12] fix: invalid job name

---
 scripts/preprocessing/create_dataset.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/preprocessing/create_dataset.py b/scripts/preprocessing/create_dataset.py
index 6595cfa..2625ba9 100644
--- a/scripts/preprocessing/create_dataset.py
+++ b/scripts/preprocessing/create_dataset.py
@@ -4,7 +4,7 @@
 COHORT = "ikem"  # "ikem", "ftn", or "knl_patos"
 
 submit_job(
-    job_name=f"ulcerative-colitis-dataset-creation-{COHORT}",
+    job_name=f"ulcerative-colitis-dataset-creation-{COHORT.replace('_', '-')}",
     username=...,
     public=False,
     cpu=2,

From fd978b347c1ac485f410597b04df137aa57d65a7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 16:14:42 +0000
Subject: [PATCH 08/12] fix: set slide_id as index and ensure nancy is an
 integer

---
 preprocessing/create_dataset.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/preprocessing/create_dataset.py b/preprocessing/create_dataset.py
index d0286fb..dbf5e49 100644
--- a/preprocessing/create_dataset.py
+++ b/preprocessing/create_dataset.py
@@ -84,6 +84,7 @@ def create_dataset(
     # IKEM has only case-level labels (FTN has one slide per case)
     on = "case_id" if institution == "ikem" else "slide_id"
     dataset_df = slides_df.join(labels_df, on=on, how="outer")
+    dataset_df.index.name = "slide_id"
 
     if institution == "ikem":
         # IKEM has 'Lokalita' and 'Diagnóza' columns
@@ -96,6 +97,7 @@ def create_dataset(
 
     dataset_df = dataset_df[["case_id", "path", "nancy"]]
     dataset_df = dataset_df.dropna()
+    dataset_df["nancy"] = dataset_df["nancy"].astype(int)
 
     return dataset_df, missing_slides, missing_labels
 

From 87113e16f3b7d2a0f47f3f0757ab2090779fad4e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Sun, 25 Jan 2026 17:23:24 +0000
Subject: [PATCH 09/12] feat: script

---
 scripts/preprocessing/create_dataset.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/scripts/preprocessing/create_dataset.py b/scripts/preprocessing/create_dataset.py
index 2625ba9..457ca7b 100644
--- a/scripts/preprocessing/create_dataset.py
+++ b/scripts/preprocessing/create_dataset.py
@@ -12,7 +12,6 @@
     script=[
         "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/ulcerative-colitis.git workdir",
         "cd workdir",
-        "git checkout feature/dataset",
         "uv sync --frozen",
         f"uv run -m preprocessing.create_dataset +data=raw/{COHORT}",
     ],

From bd0c6ac1de7b6789709eed0ab7eb7ab72070dbda Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Wed, 11 Feb 2026 08:33:30 +0000
Subject: [PATCH 10/12] fix: PR comments

---
 configs/data/raw/ftn.yaml               |  8 -------
 configs/data/raw/ikem.yaml              |  9 --------
 configs/data/raw/knl_patos.yaml         | 10 ---------
 configs/dataset/raw/ftn.yaml            |  5 +++++
 configs/dataset/raw/ikem.yaml           |  6 +++++
 configs/dataset/raw/knl_patos.yaml      |  7 ++++++
 configs/preprocessing.yaml              |  2 +-
 preprocessing/create_dataset.py         | 30 +++++++++++--------------
 scripts/preprocessing/create_dataset.py |  8 +++----
 9 files changed, 35 insertions(+), 50 deletions(-)
 delete mode 100644 configs/data/raw/ftn.yaml
 delete mode 100644 configs/data/raw/ikem.yaml
 delete mode 100644 configs/data/raw/knl_patos.yaml
 create mode 100644 configs/dataset/raw/ftn.yaml
 create mode 100644 configs/dataset/raw/ikem.yaml
 create mode 100644 configs/dataset/raw/knl_patos.yaml

diff --git a/configs/data/raw/ftn.yaml b/configs/data/raw/ftn.yaml
deleted file mode 100644
index c70f757..0000000
--- a/configs/data/raw/ftn.yaml
+++ /dev/null
@@ -1,8 +0,0 @@
-# @package _global_
-
-dataset:
-  institution: ftn
-  folder: /mnt/data/FTN/colon/IBD_AI
-  labels:
-    - IBD_AI_FTN.xlsx
-    - IBD_AI_FTN_doplnek.xlsx
\ No newline at end of file
diff --git a/configs/data/raw/ikem.yaml b/configs/data/raw/ikem.yaml
deleted file mode 100644
index 5cc8ba4..0000000
--- a/configs/data/raw/ikem.yaml
+++ /dev/null
@@ -1,9 +0,0 @@
-# @package _global_
-
-dataset:
-  institution: ikem
-  folder: /mnt/data/IKEM/colon/IBD_AI/20x
-  labels:
-    - Fab_IBD_AI_12_2024.csv
-    - IBD_AI_2.xlsx
-    - missing.xlsx
\ No newline at end of file
diff --git a/configs/data/raw/knl_patos.yaml b/configs/data/raw/knl_patos.yaml
deleted file mode 100644
index 326cbbd..0000000
--- a/configs/data/raw/knl_patos.yaml
+++ /dev/null
@@ -1,10 +0,0 @@
-# @package _global_
-
-dataset:
-  institution: knl_patos
-  folder: /mnt/data/KNL_PATOS/colon/IBD_AI
-  labels:
-    - IBD_AI_Liberec.xlsx
-    - IBD_AI_Liberec_02.xlsx
-    - IBD_AI_Liberec_10_2025.xlsx
-    - IBD_AI_Liberec_28_10_2025.xlsx
\ No newline at end of file
diff --git a/configs/dataset/raw/ftn.yaml b/configs/dataset/raw/ftn.yaml
new file mode 100644
index 0000000..ae6e96c
--- /dev/null
+++ b/configs/dataset/raw/ftn.yaml
@@ -0,0 +1,5 @@
+institution: ftn
+folder: /mnt/data/FTN/colon/IBD_AI
+labels:
+  - IBD_AI_FTN.xlsx
+  - IBD_AI_FTN_doplnek.xlsx
\ No newline at end of file
diff --git a/configs/dataset/raw/ikem.yaml b/configs/dataset/raw/ikem.yaml
new file mode 100644
index 0000000..1be47e8
--- /dev/null
+++ b/configs/dataset/raw/ikem.yaml
@@ -0,0 +1,6 @@
+institution: ikem
+folder: /mnt/data/IKEM/colon/IBD_AI/20x
+labels:
+  - Fab_IBD_AI_12_2024.csv
+  - IBD_AI_2.xlsx
+  - missing.xlsx
\ No newline at end of file
diff --git a/configs/dataset/raw/knl_patos.yaml b/configs/dataset/raw/knl_patos.yaml
new file mode 100644
index 0000000..102df9f
--- /dev/null
+++ b/configs/dataset/raw/knl_patos.yaml
@@ -0,0 +1,7 @@
+institution: knl_patos
+folder: /mnt/data/KNL_PATOS/colon/IBD_AI
+labels:
+  - IBD_AI_Liberec.xlsx
+  - IBD_AI_Liberec_02.xlsx
+  - IBD_AI_Liberec_10_2025.xlsx
+  - IBD_AI_Liberec_28_10_2025.xlsx
\ No newline at end of file
diff --git a/configs/preprocessing.yaml b/configs/preprocessing.yaml
index 6af2711..08a0372 100644
--- a/configs/preprocessing.yaml
+++ b/configs/preprocessing.yaml
@@ -6,4 +6,4 @@ defaults:
 
 dataset: ???
     
-project_dir: /mnt/projects/inflammatory_bowel_dissease/ulcerative_colitis
+project_dir: /mnt/projects/inflammatory_bowel_disease/ulcerative_colitis
diff --git a/preprocessing/create_dataset.py b/preprocessing/create_dataset.py
index dbf5e49..7c1f85d 100644
--- a/preprocessing/create_dataset.py
+++ b/preprocessing/create_dataset.py
@@ -17,12 +17,12 @@
     # HE - stain type
     # (?:_0[1-6])? - optional underscore and slide number (01 to 06)
     # .czi - file extension
-    "ikem": re.compile(r"^[0-9]{1,5}_2[1-4]_HE(?:_0[1-6])?\.czi"),
+    "ikem": re.compile(r"^[0-9]{1,5}_2[1-4]_HE(?:_0[1-6])?\.czi$"),
     # [0-9]{1,6} - case ID (1 to 6 digits) (in year scope)
     # _ - underscore separator
     # 2[0-5] - year (2020 to 2025)
     # .czi - file extension
-    "ftn": re.compile(r"[0-9]{1,6}_2[0-5]\.czi"),
+    "ftn": re.compile(r"^[0-9]{1,6}_2[0-5]\.czi"),
     # [0-9]{1,5} - case ID (1 to 5 digits) (in year scope)
     # _ - underscore separator
     # 25 - year 2025
@@ -32,14 +32,14 @@
     # HE - stain type
     # (0[1-9]|1[0-2]) - slide number (01 to 12)
     # .czi - file extension
-    "knl_patos": re.compile(r"[0-9]{1,5}_25_[A-F]_HE(0[1-9]|1[0-2])\.czi"),
+    "knl_patos": re.compile(r"^[0-9]{1,5}_25_[A-F]_HE(0[1-9]|1[0-2])\.czi$"),
 }
 
 
 def get_labels(folder_path: Path, labels: list[str]) -> pd.DataFrame:
     dfs = []
     for labels_file in labels:
-        labels_path = Path(folder_path) / labels_file
+        labels_path = folder_path / labels_file
 
         if labels_path.suffix == ".csv":
             # One labels file is in CSV format
@@ -117,19 +117,15 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
         dataset.to_csv(output_path, index=True)
         logger.log_artifact(str(output_path))
 
-        if missing_slides:
-            missing_slides_path = tmpdir_path / "missing_slides.txt"
-            with open(missing_slides_path, "w") as f:
-                for slide in missing_slides:
-                    f.write(f"{slide}\n")
-            logger.log_artifact(str(missing_slides_path))
-
-        if missing_labels:
-            missing_labels_path = tmpdir_path / "missing_labels.txt"
-            with open(missing_labels_path, "w") as f:
-                for label in missing_labels:
-                    f.write(f"{label}\n")
-            logger.log_artifact(str(missing_labels_path))
+        def _log_missing_items(items: list[str], filename: str) -> None:
+            if not items:
+                return
+            file_path = tmpdir_path / filename
+            file_path.write_text("\n".join(items) + "\n")
+            logger.log_artifact(str(file_path))
+
+        _log_missing_items(missing_slides, "missing_slides.txt")
+        _log_missing_items(missing_labels, "missing_labels.txt")
 
 
 if __name__ == "__main__":
diff --git a/scripts/preprocessing/create_dataset.py b/scripts/preprocessing/create_dataset.py
index 457ca7b..245eb97 100644
--- a/scripts/preprocessing/create_dataset.py
+++ b/scripts/preprocessing/create_dataset.py
@@ -1,19 +1,17 @@
 from kube_jobs import storage, submit_job
 
 
-COHORT = "ikem"  # "ikem", "ftn", or "knl_patos"
-
 submit_job(
-    job_name=f"ulcerative-colitis-dataset-creation-{COHORT.replace('_', '-')}",
+    job_name="ulcerative-colitis-dataset-creation-...",
     username=...,
     public=False,
     cpu=2,
     memory="4Gi",
     script=[
-        "git clone https://gitlab.ics.muni.cz/rationai/digital-pathology/pathology/ulcerative-colitis.git workdir",
+        "git clone https://github.com/RationAI/ulcerative-colitis.git workdir",
         "cd workdir",
         "uv sync --frozen",
-        f"uv run -m preprocessing.create_dataset +data=raw/{COHORT}",
+        "uv run -m preprocessing.create_dataset +data=raw/...",
     ],
     storage=[storage.secure.DATA],
 )

From 9ffea96f09f0779f92b8996ef5bb9a479b0829ce Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Wed, 11 Feb 2026 08:42:53 +0000
Subject: [PATCH 11/12] chore: dependencies

---
 pyproject.toml | 2 +-
 uv.lock        | 5 +++--
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 39445e2..9d94243 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -21,7 +21,7 @@ dependencies = [
 
 [dependency-groups]
 dev = ["mypy", "ruff", "ipykernel"]
-run = ["rationai-kube-jobs"]
+job = ["rationai-kube-jobs"]
 
 [tool.uv.sources]
 rationai-mlkit = { git = "https://gitlab.ics.muni.cz/rationai/digital-pathology/libraries/mlkit.git" }
diff --git a/uv.lock b/uv.lock
index baa2405..bd68d0c 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2065,6 +2065,7 @@ dependencies = [
     { name = "typing-extensions" },
 ]
 wheels = [
+    { url = "https://files.pythonhosted.org/packages/d3/54/a2ba279afcca44bbd320d4e73675b282fcee3d81400ea1b53934efca6462/torch-2.10.0-2-cp312-none-macosx_11_0_arm64.whl", hash = "sha256:13ec4add8c3faaed8d13e0574f5cd4a323c11655546f91fbe6afa77b57423574", size = 79498202, upload-time = "2026-02-10T21:44:52.603Z" },
     { url = "https://files.pythonhosted.org/packages/cc/af/758e242e9102e9988969b5e621d41f36b8f258bb4a099109b7a4b4b50ea4/torch-2.10.0-cp312-cp312-manylinux_2_28_aarch64.whl", hash = "sha256:5fd4117d89ffd47e3dcc71e71a22efac24828ad781c7e46aaaf56bf7f2796acf", size = 145996088, upload-time = "2026-01-21T16:24:44.171Z" },
     { url = "https://files.pythonhosted.org/packages/23/8e/3c74db5e53bff7ed9e34c8123e6a8bfef718b2450c35eefab85bb4a7e270/torch-2.10.0-cp312-cp312-manylinux_2_28_x86_64.whl", hash = "sha256:787124e7db3b379d4f1ed54dd12ae7c741c16a4d29b49c0226a89bea50923ffb", size = 915711952, upload-time = "2026-01-21T16:23:53.503Z" },
     { url = "https://files.pythonhosted.org/packages/6e/01/624c4324ca01f66ae4c7cd1b74eb16fb52596dce66dbe51eff95ef9e7a4c/torch-2.10.0-cp312-cp312-win_amd64.whl", hash = "sha256:2c66c61f44c5f903046cc696d088e21062644cbe541c7f1c4eaae88b2ad23547", size = 113757972, upload-time = "2026-01-21T16:24:39.516Z" },
@@ -2188,7 +2189,7 @@ dev = [
     { name = "mypy" },
     { name = "ruff" },
 ]
-run = [
+job = [
     { name = "rationai-kube-jobs" },
 ]
 
@@ -2213,7 +2214,7 @@ dev = [
     { name = "mypy" },
     { name = "ruff" },
 ]
-run = [{ name = "rationai-kube-jobs", git = "ssh://git@gitlab.ics.muni.cz/rationai/infrastructure/kube-jobs" }]
+job = [{ name = "rationai-kube-jobs", git = "ssh://git@gitlab.ics.muni.cz/rationai/infrastructure/kube-jobs" }]
 
 [[package]]
 name = "urllib3"

From 7d778ce79f13b99406255df72c4d12da947265b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Adam=20Kuku=C4=8Dka?= <xkukuck1@fi.muni.cz>
Date: Fri, 13 Feb 2026 15:23:03 +0000
Subject: [PATCH 12/12] fix: PR

---
 configs/dataset/raw/ftn.yaml       |  5 ++++
 configs/dataset/raw/ikem.yaml      |  8 ++++++
 configs/dataset/raw/knl_patos.yaml | 10 ++++++++
 preprocessing/create_dataset.py    | 40 ++++++------------------------
 4 files changed, 31 insertions(+), 32 deletions(-)

diff --git a/configs/dataset/raw/ftn.yaml b/configs/dataset/raw/ftn.yaml
index ae6e96c..59b9d69 100644
--- a/configs/dataset/raw/ftn.yaml
+++ b/configs/dataset/raw/ftn.yaml
@@ -1,5 +1,10 @@
 institution: ftn
 folder: /mnt/data/FTN/colon/IBD_AI
+# [0-9]{1,6} - case ID (1 to 6 digits) (in year scope)
+# _ - underscore separator
+# 2[0-5] - year (2020 to 2025)
+# .czi - file extension
+regex_pattern: ^[0-9]{1,6}_2[0-5]\.czi$
 labels:
   - IBD_AI_FTN.xlsx
   - IBD_AI_FTN_doplnek.xlsx
\ No newline at end of file
diff --git a/configs/dataset/raw/ikem.yaml b/configs/dataset/raw/ikem.yaml
index 1be47e8..4ae65db 100644
--- a/configs/dataset/raw/ikem.yaml
+++ b/configs/dataset/raw/ikem.yaml
@@ -1,5 +1,13 @@
 institution: ikem
 folder: /mnt/data/IKEM/colon/IBD_AI/20x
+# [0-9]{1,5} - case ID (1 to 5 digits) (in year scope)
+# _ - underscore separator
+# 2[1-4] - year (2021 to 2024)
+# _ - underscore separator
+# HE - stain type
+# (?:_0[1-6])? - optional underscore and slide number (01 to 06)
+# .czi - file extension
+regex_pattern: ^[0-9]{1,5}_2[1-4]_HE(?:_0[1-6])?\.czi$
 labels:
   - Fab_IBD_AI_12_2024.csv
   - IBD_AI_2.xlsx
diff --git a/configs/dataset/raw/knl_patos.yaml b/configs/dataset/raw/knl_patos.yaml
index 102df9f..450ee36 100644
--- a/configs/dataset/raw/knl_patos.yaml
+++ b/configs/dataset/raw/knl_patos.yaml
@@ -1,5 +1,15 @@
 institution: knl_patos
 folder: /mnt/data/KNL_PATOS/colon/IBD_AI
+# [0-9]{1,5} - case ID (1 to 5 digits) (in year scope)
+# _ - underscore separator
+# 25 - year 2025
+# _ - underscore separator
+# [A-F] - block identifier (A to F)
+# _ - underscore separator
+# HE - stain type
+# (0[1-9]|1[0-2]) - slide number (01 to 12)
+# .czi - file extension
+regex_pattern: ^[0-9]{1,5}_25_[A-F]_HE(0[1-9]|1[0-2])\.czi$
 labels:
   - IBD_AI_Liberec.xlsx
   - IBD_AI_Liberec_02.xlsx
diff --git a/preprocessing/create_dataset.py b/preprocessing/create_dataset.py
index 7c1f85d..af2ef37 100644
--- a/preprocessing/create_dataset.py
+++ b/preprocessing/create_dataset.py
@@ -9,33 +9,6 @@
 from rationai.mlkit.lightning.loggers import MLFlowLogger
 
 
-REGEX = {
-    # [0-9]{1,5} - case ID (1 to 5 digits) (in year scope)
-    # _ - underscore separator
-    # 2[1-4] - year (2021 to 2024)
-    # _ - underscore separator
-    # HE - stain type
-    # (?:_0[1-6])? - optional underscore and slide number (01 to 06)
-    # .czi - file extension
-    "ikem": re.compile(r"^[0-9]{1,5}_2[1-4]_HE(?:_0[1-6])?\.czi$"),
-    # [0-9]{1,6} - case ID (1 to 6 digits) (in year scope)
-    # _ - underscore separator
-    # 2[0-5] - year (2020 to 2025)
-    # .czi - file extension
-    "ftn": re.compile(r"^[0-9]{1,6}_2[0-5]\.czi"),
-    # [0-9]{1,5} - case ID (1 to 5 digits) (in year scope)
-    # _ - underscore separator
-    # 25 - year 2025
-    # _ - underscore separator
-    # [A-F] - block identifier (A to F)
-    # _ - underscore separator
-    # HE - stain type
-    # (0[1-9]|1[0-2]) - slide number (01 to 12)
-    # .czi - file extension
-    "knl_patos": re.compile(r"^[0-9]{1,5}_25_[A-F]_HE(0[1-9]|1[0-2])\.czi$"),
-}
-
-
 def get_labels(folder_path: Path, labels: list[str]) -> pd.DataFrame:
     dfs = []
     for labels_file in labels:
@@ -59,10 +32,10 @@ def get_labels(folder_path: Path, labels: list[str]) -> pd.DataFrame:
     return labels_df
 
 
-def get_slides(folder_path: Path, institution: str) -> pd.DataFrame:
+def get_slides(folder_path: Path, pattern: re.Pattern) -> pd.DataFrame:
     slides = []
     for slide_path in folder_path.iterdir():
-        if not REGEX[institution].fullmatch(slide_path.name):
+        if not pattern.fullmatch(slide_path.name):
             continue
         case_id = "_".join(slide_path.stem.split("_")[:2])
 
@@ -75,11 +48,11 @@ def get_slides(folder_path: Path, institution: str) -> pd.DataFrame:
 
 
 def create_dataset(
-    folder: str, labels: list[str], institution: str
+    folder: str, labels: list[str], institution: str, pattern: re.Pattern
 ) -> tuple[pd.DataFrame, list[str], list[str]]:
     folder_path = Path(folder)
     labels_df = get_labels(folder_path, labels)
-    slides_df = get_slides(folder_path, institution)
+    slides_df = get_slides(folder_path, pattern)
 
     # IKEM has only case-level labels (FTN has one slide per case)
     on = "case_id" if institution == "ikem" else "slide_id"
@@ -107,7 +80,10 @@ def create_dataset(
 @autolog
 def main(config: DictConfig, logger: MLFlowLogger) -> None:
     dataset, missing_slides, missing_labels = create_dataset(
-        config.dataset.folder, config.dataset.labels, config.dataset.institution
+        config.dataset.folder,
+        config.dataset.labels,
+        config.dataset.institution,
+        re.compile(config.dataset.regex_pattern),
     )
 
     with tempfile.TemporaryDirectory() as tmpdir: