Prerequisites

This workflow version supports only Whole-Slide Images (WSIs) in the MIRAX format. It is specifically tailored for prostate cancer needle biopsies stained with hematoxylin and eosin (H&E).

If you do not have access to suitable WSIs, you can use slides from an open dataset provided by the Department of Information Technology and SciLifeLab, Uppsala University and the Department of Medical Biosciences, Pathology, Umeå University. This dataset is described in the following publication:

Chelebian, E., Avenel, C., Järemo, H., Andersson, P., Wählby, C., & Bergh, A. (2025). A clinical prostate biopsy dataset with undetected cancer. Scientific Data, 12(1), 423.
DOI:10.1038/s41597-025-04758-7

You can download the dataset from DOI:10.57804/epa0-8v59

To be imported within the platform, slides names must adhere to the following pattern:

<case_id>-<slide_index>[.<ext>]

Since the slides in this dataset use a different naming convention, we provide a helper tool to rename and organize the files into a compatible format.
To rename the slides, follow these steps:

git clone https://gist.github.com/6ea4d6c0d0a07e8486c6c1613051c03a.git rename_slides
cd rename_slides
python rename_umea_dataset.py <SLIDES_INPUT_DIR> <SLIDES_OUTPUT_DIR>

where SLIDES_INPUT_DIR is the path to the original dataset slides, and SLIDES_OUTPUT_DIR is the destination directory where the renamed slides will be copied, conforming to the standard platform naming convention.
To move (instead of copy) the slides, add the --move option:

python rename_umea_dataset.py --move <SLIDES_INPUT_DIR> <SLIDES_OUTPUT_DIR>

To facilitate the process, we suggest to use the $INPUT_DIR directory defined in the .env file as SLIDE_OUTPUT_DIR.

Execute workflows

After starting the platform services (using ./compose.sh), place the WSIs to be analyzed in the $INPUT_DIR directory, which is defined in your .env file.

Use slide_importer/local.py to run either:

  • the basic_pipeline for slide ingestion and tissue segmentation (H&E WSIs), or
  • the more advanced pca_pipeline, which also performs prostate cancer classification.
cd slide-importer
poetry install
source ../.env
poetry run python slide_importer/local.py basic_pipeline  --user $AIRFLOW_USER -P $AIRFLOW_PASSWORD --server-url http://localhost:$AIRFLOW_WEBSERVER_PORT  --wait --params '{"level": 8}'
# or 
poetry run python slide_importer/local.py pca_pipeline --user $AIRFLOW_USER -P $AIRFLOW_PASSWORD --server-url http://localhost:$AIRFLOW_WEBSERVER_PORT -p '{ "tissue-high-level": 8, "tissue-high-filter": "tissue_low>1", "tumor-filter": "tissue_low>1", "gpu": null}'  --wait

Parameters for the ‘basic_pipeline’ are defined in cwl/tissue_segmentation_workflow.cwl, while the ones for the ‘pca_pipeline’ are defined in cwl/pca_classification_workflow.cwl.

Inspect outputs

The outputs of a workflow run are located in $CWL_OUTPUTS_FOLDER<WORKFLOW_NAME><WORKFLOW_RUN_NAME>. If the workflow is based on CWL, $CWL_OUTPUTS_FOLDER<WORKFLOW_NAME><WORKFLOW_RUN_NAME>/rocrate dir is also present, containing the RO-Crate that tracks the provenance of the given workflow execution. It contains all the information needed for re-running the workflow. You can read and validate it using libraries such rocrate and rocrate-validator.