Tutorials#
MI Visium#
The following tutorials use data from the Myocardial Infarction (MI) atlas [Kuppe et al., 2022]. The first one demonstrates how NicheSphere identifies differential co-localization niches and associated biological processes related to ischemia. Then, the second one uses PILOT to infer a disease trajectory at the sample level.
PIC-seq#
The following tutorial applies NicheSphere to fibrosis mouse models (TPO) bone marrow PIC-seq data [Gleitz et al., 2026] to identify fibrosis specific co-localization niches and associated biological processes.
CODEX#
The following tutorial applies NicheSphere to fibrosis mouse models (Ctrl, ThPO, MPL) spleen CODEX data [Dugué et al., 2026] to identify fibrosis specific co-localization niches. Then it uses PILOT to infer a disease trajectory at the sample level.
Data required to run all the tutorials can be downloaded from Zenodo: https://doi.org/10.5281/zenodo.22678370