diff --git a/.mypy.ini b/.mypy.ini
index abd4983..d895db7 100644
--- a/.mypy.ini
+++ b/.mypy.ini
@@ -3,4 +3,4 @@ strict = True
 ignore_missing_imports = True
 disallow_untyped_calls = False
 disable_error_code = no-any-return
-exclude = scripts
\ No newline at end of file
+exclude = ^(scripts|project_name)/
\ No newline at end of file
diff --git a/configs/dataset/processed/ftn.yaml b/configs/dataset/processed/ftn.yaml
new file mode 100644
index 0000000..49f2ea6
--- /dev/null
+++ b/configs/dataset/processed/ftn.yaml
@@ -0,0 +1,5 @@
+defaults:
+  - /dataset/raw/ftn@_here_
+  - _self_
+
+uri: mlflow-artifacts:/86/d2b2f1835fc647e2ba3639ce606f4768/artifacts/dataset.csv
\ No newline at end of file
diff --git a/configs/dataset/processed/ikem.yaml b/configs/dataset/processed/ikem.yaml
new file mode 100644
index 0000000..d230341
--- /dev/null
+++ b/configs/dataset/processed/ikem.yaml
@@ -0,0 +1,5 @@
+defaults:
+  - /dataset/raw/ikem@_here_
+  - _self_
+
+uri: mlflow-artifacts:/86/7c6e7cc142494d45b6513185318d4462/artifacts/dataset.csv
\ No newline at end of file
diff --git a/configs/dataset/processed/knl_patos.yaml b/configs/dataset/processed/knl_patos.yaml
new file mode 100644
index 0000000..9f575c8
--- /dev/null
+++ b/configs/dataset/processed/knl_patos.yaml
@@ -0,0 +1,5 @@
+defaults:
+  - /dataset/raw/knl_patos@_here_
+  - _self_
+
+uri: mlflow-artifacts:/86/f690f64ded624da9a7150a7a92385aec/artifacts/dataset.csv
\ No newline at end of file
diff --git a/configs/preprocessing/tissue_masks.yaml b/configs/preprocessing/tissue_masks.yaml
new file mode 100644
index 0000000..284940d
--- /dev/null
+++ b/configs/preprocessing/tissue_masks.yaml
@@ -0,0 +1,11 @@
+# @package _global_
+
+level: 3
+max_concurrent: 64
+artifact_path: tissue_masks
+
+metadata:
+  run_name: "🎭 Tissue Masks: ${dataset.institution}"
+  description: Tissue masks for ${dataset.institution} at level ${level}
+  hyperparams:
+    level: ${level}
\ No newline at end of file
diff --git a/preprocessing/.gitkeep b/preprocessing/.gitkeep
deleted file mode 100644
index e69de29..0000000
diff --git a/preprocessing/create_dataset.py b/preprocessing/create_dataset.py
index af2ef37..551dd39 100644
--- a/preprocessing/create_dataset.py
+++ b/preprocessing/create_dataset.py
@@ -32,7 +32,7 @@ def get_labels(folder_path: Path, labels: list[str]) -> pd.DataFrame:
     return labels_df
 
 
-def get_slides(folder_path: Path, pattern: re.Pattern) -> pd.DataFrame:
+def get_slides(folder_path: Path, pattern: re.Pattern[str]) -> pd.DataFrame:
     slides = []
     for slide_path in folder_path.iterdir():
         if not pattern.fullmatch(slide_path.name):
@@ -48,7 +48,7 @@ def get_slides(folder_path: Path, pattern: re.Pattern) -> pd.DataFrame:
 
 
 def create_dataset(
-    folder: str, labels: list[str], institution: str, pattern: re.Pattern
+    folder: str, labels: list[str], institution: str, pattern: re.Pattern[str]
 ) -> tuple[pd.DataFrame, list[str], list[str]]:
     folder_path = Path(folder)
     labels_df = get_labels(folder_path, labels)
diff --git a/preprocessing/tissue_masks.py b/preprocessing/tissue_masks.py
new file mode 100644
index 0000000..5590edf
--- /dev/null
+++ b/preprocessing/tissue_masks.py
@@ -0,0 +1,56 @@
+from pathlib import Path
+from tempfile import TemporaryDirectory
+from typing import cast
+
+import hydra
+import pandas as pd
+import pyvips
+import ray
+from mlflow.artifacts import download_artifacts
+from omegaconf import DictConfig
+from openslide import OpenSlide
+from rationai.masks import (
+    process_items,
+    slide_resolution,
+    tissue_mask,
+    write_big_tiff,
+)
+from rationai.mlkit import autolog, with_cli_args
+from rationai.mlkit.lightning.loggers import MLFlowLogger
+
+
+@ray.remote(memory=4 * 1024**3)
+def process_slide(slide_path: str, level: int, output_path: Path) -> None:
+    with OpenSlide(slide_path) as slide:
+        mpp_x, mpp_y = slide_resolution(slide, level)
+
+    image = cast("pyvips.Image", pyvips.Image.new_from_file(slide_path, level=level))
+    mask = tissue_mask(image, mpp=(mpp_x + mpp_y) / 2)
+    mask_path = output_path / Path(slide_path).with_suffix(".tiff").name
+
+    write_big_tiff(mask, path=mask_path, mpp_x=mpp_x, mpp_y=mpp_y)
+
+
+@with_cli_args(["+preprocessing=tissue_masks"])
+@hydra.main(config_path="../configs", config_name="preprocessing", version_base=None)
+@autolog
+def main(config: DictConfig, logger: MLFlowLogger) -> None:
+    dataset = pd.read_csv(download_artifacts(config.dataset.uri))
+
+    with TemporaryDirectory() as output_dir:
+        process_items(
+            dataset["path"],
+            process_item=process_slide,
+            fn_kwargs={
+                "level": config.level,
+                "output_path": Path(output_dir),
+            },
+            max_concurrent=config.max_concurrent,
+        )
+
+        logger.log_artifacts(local_dir=output_dir, artifact_path=config.artifact_path)
+
+
+if __name__ == "__main__":
+    with ray.init(runtime_env={"excludes": [".git", ".venv"]}):
+        main()
diff --git a/pyproject.toml b/pyproject.toml
index 9d94243..657fd36 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,6 +14,7 @@ dependencies = [
     "pandas>=2.3.3",
     "pyvips<3.1",
     "rationai-mlkit",
+    "rationai-masks",
     "ray>=2.52.1",
     "torch>=2.9.0",
     "torchmetrics>=1.8.2",
@@ -25,4 +26,5 @@ job = ["rationai-kube-jobs"]
 
 [tool.uv.sources]
 rationai-mlkit = { git = "https://gitlab.ics.muni.cz/rationai/digital-pathology/libraries/mlkit.git" }
+rationai-masks = { git = "https://gitlab.ics.muni.cz/rationai/digital-pathology/libraries/masks.git" }
 rationai-kube-jobs = { git = "ssh://git@gitlab.ics.muni.cz/rationai/infrastructure/kube-jobs" }
diff --git a/scripts/preprocessing/create_dataset.py b/scripts/preprocessing/create_dataset.py
index 245eb97..79ec7ba 100644
--- a/scripts/preprocessing/create_dataset.py
+++ b/scripts/preprocessing/create_dataset.py
@@ -11,7 +11,7 @@
         "git clone https://github.com/RationAI/ulcerative-colitis.git workdir",
         "cd workdir",
         "uv sync --frozen",
-        "uv run -m preprocessing.create_dataset +data=raw/...",
+        "uv run -m preprocessing.create_dataset +dataset=raw/...",
     ],
     storage=[storage.secure.DATA],
 )
diff --git a/scripts/preprocessing/tissue_masks.py b/scripts/preprocessing/tissue_masks.py
new file mode 100644
index 0000000..2da75b2
--- /dev/null
+++ b/scripts/preprocessing/tissue_masks.py
@@ -0,0 +1,18 @@
+from kube_jobs import storage, submit_job
+
+
+submit_job(
+    job_name="ulcerative-colitis-tissue-masks-...",
+    username=...,
+    public=False,
+    cpu=64,
+    memory="32Gi",
+    shm="16Gi",
+    script=[
+        "git clone https://github.com/RationAI/ulcerative-colitis.git workdir",
+        "cd workdir",
+        "uv sync --frozen",
+        "uv run --active -m preprocessing.tissue_masks +dataset=processed/...",
+    ],
+    storage=[storage.secure.DATA],
+)
diff --git a/uv.lock b/uv.lock
index bd68d0c..4178183 100644
--- a/uv.lock
+++ b/uv.lock
@@ -2177,6 +2177,7 @@ dependencies = [
     { name = "openpyxl" },
     { name = "pandas" },
     { name = "pyvips" },
+    { name = "rationai-masks" },
     { name = "rationai-mlkit" },
     { name = "ray" },
     { name = "torch" },
@@ -2202,6 +2203,7 @@ requires-dist = [
     { name = "openpyxl", specifier = ">=3.1.5" },
     { name = "pandas", specifier = ">=2.3.3" },
     { name = "pyvips", specifier = "<3.1" },
+    { name = "rationai-masks", git = "https://gitlab.ics.muni.cz/rationai/digital-pathology/libraries/masks.git" },
     { name = "rationai-mlkit", git = "https://gitlab.ics.muni.cz/rationai/digital-pathology/libraries/mlkit.git" },
     { name = "ray", specifier = ">=2.52.1" },
     { name = "torch", specifier = ">=2.9.0" },