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.

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.