MITI Minimum Information guidelines for highly multiplexed tissue images

2 code implementations • 21 Aug 2021 • Denis Schapiro, Clarence Yapp, Artem Sokolov, Sheila M. Reynolds, Yu-An Chen, Damir Sudar, Yubin Xie, Jeremy L. Muhlich, Raquel Arias-Camison, Sarah Arena, Adam J. Taylor, Milen Nikolov, Madison Tyler, Jia-Ren Lin, Erik A. Burlingame, Human Tumor Atlas Network, Young H. Chang, Samouil L Farhi, Vésteinn Thorsson, Nithya Venkatamohan, Julia L. Drewes, Dana Pe'er, David A. Gutman, Markus D. Herrmann, Nils Gehlenborg, Peter Bankhead, Joseph T. Roland, John M. Herndon, Michael P. Snyder, Michael Angelo, Garry Nolan, Jason R. Swedlow, Nikolaus Schultz, Daniel T. Merrick, Sarah A. Mazzilli, Ethan Cerami, Scott J. Rodig, Sandro Santagata, Peter K. Sorger

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release.

Common Limitations of Image Processing Metrics: A Picture Story

1 code implementation • 12 Apr 2021 • Annika Reinke, Minu D. Tizabi, Carole H. Sudre, Matthias Eisenmann, Tim Rädsch, Michael Baumgartner, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Peter Bankhead, Arriel Benis, M. Jorge Cardoso, Veronika Cheplygina, Evangelia Christodoulou, Beth Cimini, Gary S. Collins, Keyvan Farahani, Bram van Ginneken, Ben Glocker, Patrick Godau, Fred Hamprecht, Daniel A. Hashimoto, Doreen Heckmann-Nötzel, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Alexandros Karargyris, Alan Karthikesalingam, Bernhard Kainz, Emre Kavur, Hannes Kenngott, Jens Kleesiek, Thijs Kooi, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A. Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L. Martel, Peter Mattson, Erik Meijering, Bjoern Menze, David Moher, Karel G. M. Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, M. Alican Noyan, Jens Petersen, Gorkem Polat, Nasir Rajpoot, Mauricio Reyes, Nicola Rieke, Michael Riegler, Hassan Rivaz, Julio Saez-Rodriguez, Clarisa Sanchez Gutierrez, Julien Schroeter, Anindo Saha, Shravya Shetty, Maarten van Smeden, Bram Stieltjes, Ronald M. Summers, Abdel A. Taha, Sotirios A. Tsaftaris, Ben van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Annette Kopp-Schneider, Paul Jäger, Lena Maier-Hein

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation.

Instance Segmentation object-detection +2