Alma Anderson and Joakim Lundeberg. Sepal: identifying transcript profiles with spatial patterns by diffusion-based modeling. Bioinformatics, 2021. doi:10.1093/bioinformatics/btab164.


Adrian Baddeley, Ege Rubak, and Rolf Turner. Spatial Point Patterns: Methodology and Applications with R. CRC Press, November 2015.


Tommaso Biancalani, Gabriele Scalia, Lorenzo Buffoni, Raghav Avasthi, Ziqing Lu, Aman Sanger, Neriman Tokcan, Charles R. Vanderburg, Asa Segerstolpe, Meng Zhang, Inbal Avraham-Davidi, Sanja Vickovic, Mor Nitzan, Sai Ma, Jason Buenrostro, Nik Bear Brown, Duccio Fanelli, Xiaowei Zhuang, Evan Z. Macosko, and Aviv Regev. Deep learning and alignment of spatially-resolved whole transcriptomes of single cells in the mouse brain with tangram. bioRxiv, 2020. URL:, doi:10.1101/2020.08.29.272831.


Mirjana Efremova, Miquel Vento-Tormo, Sarah A Teichmann, and Roser Vento-Tormo. Cellphonedb: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes. Nature protocols, 15(4):1484–1506, 2020. doi:10.1038/s41596-020-0292-x.


Aric Hagberg, Pieter Swart, and Daniel S Chult. Exploring network structure, dynamics, and function using networkx. Technical Report, Los Alamos National Lab.(LANL), Los Alamos, NM (United States), 2008. URL:


Kenji Kamimoto, Christy M. Hoffmann, and Samantha A. Morris. Celloracle: dissecting cell identity via network inference and in silico gene perturbation. bioRxiv, 2020. doi:10.1101/2020.02.17.947416.


Giovanni Palla, Hannah Spitzer, Michal Klein, David Fischer, Anna Christina Schaar, Louis Benedikt Kuemmerle, Sergei Rybakov, Ignacio L. Ibarra, Olle Holmberg, Isaac Virshup, Mohammad Lotfollahi, Sabrina Richter, and Fabian J. Theis. Squidpy: a scalable framework for spatial omics analysis. Nature Methods, 19(2):171–178, Feb 2022. doi:10.1038/s41592-021-01358-2.


Sergio J Rey and Luc Anselin. Pysal: a python library of spatial analytical methods. In Handbook of applied spatial analysis, pages 175–193. Springer, 2010. doi:10.1007/978-3-642-03647-7_11.


Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers. Cell detection with star-convex polygons. In Medical Image Computing and Computer Assisted Intervention - MICCAI 2018 - 21st International Conference, Granada, Spain, September 16-20, 2018, Proceedings, Part II, 265–273. 2018. doi:10.1007/978-3-030-00934-2_30.


Carsen Stringer, Tim Wang, Michalis Michaelos, and Marius Pachitariu. Cellpose: a generalist algorithm for cellular segmentation. Nature Methods, 18(1):100–106, 2021.


Bosiljka Tasic, Zizhen Yao, Lucas T Graybuck, Kimberly A Smith, Thuc Nghi Nguyen, Darren Bertagnolli, Jeff Goldy, Emma Garren, Michael N Economo, Sarada Viswanathan, and others. Shared and distinct transcriptomic cell types across neocortical areas. Nature, 563(7729):72–78, 2018.


Dénes Türei, Tamás Korcsmáros, and Julio Saez-Rodriguez. Omnipath: guidelines and gateway for literature-curated signaling pathway resources. Nature methods, 13(12):966–967, 2016. doi:10.1038/nmeth.4077.


Martin Weigert, Uwe Schmidt, Robert Haase, Ko Sugawara, and Gene Myers. Star-convex polyhedra for 3d object detection and segmentation in microscopy. In The IEEE Winter Conference on Applications of Computer Vision (WACV). March 2020. doi:10.1109/WACV45572.2020.9093435.