Supported modalities

As of March 2026, only the modalities below are supported by K-Pro Data Model:

• Clinical data

• Molecular data:

  • Bulk RNA seq

  • Single / nuclei cell RNA seq

  • Spatial transcriptomics (VisiumSD)

  • Whole Exome Sequencing

  • Proteomics

• Histology - slide annotation linked to a patient

Extra modalities / technologies are available upon request. By default K-Pro expects to receive processed data (in the format of count matrixes for example for bulk and single cell data), however Owkin has also developed in-house processing pipeline that can process raw files for both bulk RNAseq, Chromium single-cell and Visium spatial sequencing.

Clinical data

Standard clinical data formats are supported (.csv, .tsv, .xlsx, …).

Molecular data

Here is a table of supported modalities and source formats.

Modalities	Formats
Bulk RNAseq	Count matrix (.txt / .tsv / .csv); AnnData (.h5ad)
Single cell RNAseq	Matrix Market (.mtx + .tsv); HDF5 (.h5); AnnData (.h5ad); Seurat object (.rds)
Spatial transcriptomics	Matrix Market (.mtx + barcodes.tsv + features.tsv); HDF5 (.h5); AnnData (.h5ad); Seurat object (.rds)
WES / WGS	VCF
Proteomics	Normalized intensity matrix (.txt / .tsv / .csv); AnnData (.h5ad)

Imaging data

Here is a table of supported modalities and formats.

Modalities	Formats
Histology (H&E WSI)	.tif, .tiff, .svs, .dcm, .svs, .ndpi, .mrxs
Immunohistochemistry (IHC)	.tif, .tiff, .svs, .dcm, .svs, .ndpi, .mrxs

Note that Owkin developed several imaging processing pipelines that can be applied to imaging data, including:

• Cell segmentation and cell annotation via the HIPE model . Resulting cell-type quantifications are then saved (format: .csv) and used by K pro.

• IHC score extraction with proprietary models (e.g., HER2 score, NMR, etc.). Resulting patient-level scores are then saved and used by K-pro.

Self Supervised Features extraction via Foundation Models: slides are divided into tiles from which latent representations are computed, saved (format: .npy)