Welcome to NicheSphere’s documentation!#
NicheSphere is an sc-verse compatible Python library which allows the user to find differential co-localization domains / niches based on cell type pair co-localization probabilities in different conditions. Cell type pair co-localization probabilities can be obtained in different ways, for example, through deconvolution of spatial transcriptomics / PIC-seq data (getting the probabilities of finding each cell type in each spot / multiplet) ; or counting cell boundaries overlaps for each cell type pair in single cell spatial data (MERFISH , CODEX …).
It also offers the possibility to look at biological process based differential communication among differential co-localization domains based on Ligand-Receptor pairs expression data, such as results from pyCrossTalkeR.
Installation#
Citation#
If you use NicheSphere in your research, please cite our paper [Gleitz et al., 2026]:
NicheSphere reveals Spp1⁺ macrophages as central hubs coordinating fibrotic remodeling in myeloproliferative neoplasms
Hélène F.E. Gleitz, Mayra L. Ruiz Tejada Segura, James S. Nagai, Stijn N.R. Fuchs, Gerjanne Vroeg in de Wei, Inge A.M. Snoeren, Giulia Cesaro, Iris J. Bakker, Marta Gargallo Garasa, Jessica E. Pritchard, Tesa Klenovšek, Stephani Schmitz, Lina Schmidt, Eric Bindels, Twan Lammers, Joost Gribnau, Hind Medyouf, Kai Markus Schneider, Carolin V. Schneider, Rafael Kramann, Ivan G. Costa, Rebekka K. Schneider.
bioRxiv 2026.03.16.711605
@misc{gleitz_nichesphere_2026,
title = {{NicheSphere} reveals {Spp1}⁺ macrophages as central hubs coordinating fibrotic remodeling in myeloproliferative neoplasms},
author = {Gleitz, Hélène F. E. and Segura, Mayra L. Ruiz Tejada and Nagai, James S. and Fuchs, Stijn N. R. and Wei, Gerjanne Vroeg in de and Snoeren, Inge A. M. and Cesaro, Giulia and Bakker, Iris J. and Garasa, Marta Gargallo and Pritchard, Jessica E. and Klenovšek, Tesa and Schmitz, Stephani and Schmidt, Lina and Bindels, Eric and Lammers, Twan and Gribnau, Joost and Medyouf, Hind and Schneider, Kai Markus and Schneider, Carolin V. and Kramann, Rafael and Costa, Ivan G. and Schneider, Rebekka K.},
publisher = {bioRxiv},
year = {2026},
month = mar,
doi = {10.64898/2026.03.16.711605},
url = {https://www.biorxiv.org/content/10.64898/2026.03.16.711605v1}
}
Tutorials#
Docker image and summarized analysis tutorial#
We provide access to a Docker image, available at: sysbiobig/ismb-eccb-2025-tutorial-vt3/container_registry. The Docker image comes preconfigured with all necessary libraries, tools, and software required to follow the hands-on exercises. Additionally, the repository at sysbiobig/ismb-eccb-2025-tutorial-vt3 contains a summarized NicheSphere co-localization + communication analysis tutorial.