Workshop 'Spatial transcriptomics data analysis in Python' - 1.1 (squidpy)

Speakers in this part of the workshop: Fabian Theis & Giovanni Palla (Helmholtz Munich, Germany)

The workshop was held by Giovanni Palla (Helmholtz Munich, Germany), David Fischer (Helmholtz Munich, Germany), Anna Schaar (TUM, Germany), Alma Andersson (KTH, Sweden), Vitalii Kleshchevnikov (Wellcome Sanger Institute, UK), Johanna Klughammer (LMU, Germany) and Fabian Theis (Helmholtz Munich, Germany).

It covered the analysis of spatial transcriptomics data in Python, with tools like squidpy, node-centric expression models (ncem) as well as deconvolution (cell2location) and registration methods (eggplant). The workshop introduced the participants to both theoretical concepts as well as hands-on tutorials for the analysis of spatial transcriptomics data. Publicly available data was available for this purpose, but users were welcome to analyze their own data in the context of the workshop.

Basic python and scanpy knowledge required.

0:00 Welcome & Introduction (Fabian Theis, Helmholtz Munich)
31:27 squidpy Introduction & Tutorial (Giovanni Palla, Helmholtz Munich)