Olle Holmberg

Squidpy extends Scanpy/AnnData with spatial neighbor graphs and a lazy-loading image container, enabling spatial statistics, ligand-receptor tests, image features, and ~10-fold faster neighborhood enrichment than Giotto.

Sfaira provides a data and model zoo for single-cell RNA-seq, enabling fast reuse of pre-trained models and datasets across human and mouse tissues.

The paper proposes a self-supervised method to predict retinal thickness from fundus images, enabling efficient diabetic retinopathy classification with fewer annotations.