ATLIS is an interpretable spatial–temporal modeling framework in which cell-type composition defines an interpretable latent space that anchors spatial organization and temporal evolution in multi-slice spatial transcriptomics data.
You can install the released version of ATLIS from Github with the following code:
git clone https://github.com/YMa-lab/ATLIS.git
Mouse dorsal brain example notebook
Zebrafish development example notebook
Data download instructions can be found within each real data notebook.
Wenjun Zhao# and Ying Ma#, ATLIS: Anchored Tissue Landscapes in an Interpretable Latent Space. 2026