References

AL21

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

BRT15

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

BSB+20

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: https://www.biorxiv.org/content/early/2020/09/24/2020.08.29.272831, doi:10.1101/2020.08.29.272831.

EVTTVT20

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.

GHP18

Gabriele Gut, Markus D Herrmann, and Lucas Pelkmans. Multiplexed protein maps link subcellular organization to cellular states. Science, 2018. doi:10.1126/science.aar7042.

HSSC08

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: https://www.osti.gov/biblio/960616.

HMM+20

Felix J. Hartmann, Dunja Mrdjen, Erin McCaffrey, David R. Glass, Noah F. Greenwald, Anusha Bharadwaj, Zumana Khair, Alex Baranski, Reema Baskar, Michael Angelo, and Sean C. Bendall. Multiplexed single-cell metabolic profiles organize the spectrum of cytotoxic human t cells. bioRxiv, 2020. doi:10.1101/2020.01.17.909796.

JFZ+20

Hartland W Jackson, Jana R Fischer, Vito RT Zanotelli, H Raza Ali, Robert Mechera, Savas D Soysal, Holger Moch, Simone Muenst, Zsuzsanna Varga, Walter P Weber, and others. The single-cell pathology landscape of breast cancer. Nature, 578(7796):615–620, 2020.

KHM20

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.

LGM+20

Tim Lohoff, Shila Ghazanfar, Alsu Missarova, Noushin Koulena, Nico Pierson, Jonathan A Griffiths, Evan S Bardot, Chee-Huat Linus Eng, Richard CV Tyser, Ricard Argelaguet, and others. Highly multiplexed spatially resolved gene expression profiling of mouse organogenesis. bioRxiv, 2020.

MBME+18

Jeffrey R Moffitt, Dhananjay Bambah-Mukku, Stephen W Eichhorn, Eric Vaughn, Karthik Shekhar, Julio D Perez, Nimrod D Rubinstein, Junjie Hao, Aviv Regev, Catherine Dulac, and Xiaowei Zhuang. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science, 2018. doi:10.1126/science.aau5324.

PSK+22

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.

RA10

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.

SWBM18

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.

SMK+20

Robert R Stickels, Evan Murray, Pawan Kumar, Jilong Li, Jamie L Marshall, Daniela J Di Bella, Paola Arlotta, Evan Z Macosko, and Fei Chen. Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2. Nat. Biotechnol., 2020. doi:10.1038/s41587-020-0739-1.

SWMP21

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

TYG+18

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.

TureiKorcsmarosSR16

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.

VLK+20

Eva Gracia Villacampa, Ludvig Larsson, Linda Kvastad, Alma Andersson, Joseph Carlson, and Joakim Lundeberg. Genome-wide spatial expression profiling in ffpe tissues. bioRxiv, 2020. URL: https://www.biorxiv.org/content/early/2020/07/25/2020.07.24.219758, doi:10.1101/2020.07.24.219758.

WSH+20

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.