Bibliography#
Levin M Moser, Nodar Gogoberidze, Andréa Papaleo, Alice Lucas, David Dao, Christoph A Friedrich, Lassi Paavolainen, Csaba Molnar, David R Stirling, Jane Hung, Rex Wang, Callum Tromans-Coia, Bin Li, Edward L Evans, Kevin W Eliceiri, Peter Horvath, Anne E Carpenter, and Beth A Cimini. Piximi - an images to discovery web tool for bioimages and beyond. bioRxiv, pages 2024.06.03.597232, June 2024.
Sigrun M Gustafsdottir, Vebjorn Ljosa, Katherine L Sokolnicki, J Anthony Wilson, Deepika Walpita, Melissa M Kemp, Kathleen Petri Seiler, Hyman A Carrel, Todd R Golub, Stuart L Schreiber, Paul A Clemons, Anne E Carpenter, and Alykhan F Shamji. Multiplex cytological profiling assay to measure diverse cellular states. PLoS One, 8(12):e80999, December 2013.
David R Stirling, Madison J Swain-Bowden, Alice M Lucas, Anne E Carpenter, Beth A Cimini, and Allen Goodman. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics, 22(1):433, September 2021.
Curtis T Rueden, Jeanelle Ackerman, Ellen T Arena, Jan Eglinger, Beth A Cimini, Allen Goodman, Anne E Carpenter, and Kevin W Eliceiri. Scientific community image forum: a discussion forum for scientific image software. PLoS Biol., 17(6):e3000340, June 2019.
Rebecca A Senft, Barbara Diaz-Rohrer, Pina Colarusso, Lucy Swift, Nasim Jamali, Helena Jambor, Thomas Pengo, Craig Brideau, Paula Montero Llopis, Virginie Uhlmann, Jason Kirk, Kevin Andrew Gonzales, Peter Bankhead, Edward L Evans, III, Kevin W Eliceiri, and Beth A Cimini. A biologist's guide to planning and performing quantitative bioimaging experiments. PLoS Biol., 21(6):e3002167, June 2023.
Christopher Schmied, Michael S Nelson, Sergiy Avilov, Gert-Jan Bakker, Cristina Bertocchi, Johanna Bischof, Ulrike Boehm, Jan Brocher, Mariana T Carvalho, Catalin Chiritescu, Jana Christopher, Beth A Cimini, Eduardo Conde-Sousa, Michael Ebner, Rupert Ecker, Kevin Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grunwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia Le Dévédec, Sylvie Le Guyader, Penghuan Liu, Gabriel G Martins, Aastha Mathur, Kota Miura, Paula Montero Llopis, Roland Nitschke, Alison North, Adam C Parslow, Alex Payne-Dwyer, Laure Plantard, Rizwan Ali, Britta Schroth-Diez, Lucas Schütz, Ryan T Scott, Arne Seitz, Olaf Selchow, Ved P Sharma, Martin Spitaler, Sathya Srinivasan, Caterina Strambio-De-Castillia, Douglas Taatjes, Christian Tischer, and Helena Klara Jambor. Community-developed checklists for publishing images and image analyses. Nat. Methods, 21(2):170–181, February 2024.
Lena Maier-Hein, Annika Reinke, Patrick Godau, Minu D Tizabi, Florian Buettner, Evangelia Christodoulou, Ben Glocker, Fabian Isensee, Jens Kleesiek, Michal Kozubek, Mauricio Reyes, Michael A Riegler, Manuel Wiesenfarth, A Emre Kavur, Carole H Sudre, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, Tim Rädsch, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary S Collins, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Robert Haase, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, Florian Kofler, Annette Kopp-Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern Menze, Karel G M Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gaël Varoquaux, and Paul F Jäger. Metrics reloaded: recommendations for image analysis validation. Nat. Methods, 21(2):195–212, February 2024.
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Acion, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Florian Buettner, M Jorge Cardoso, Veronika Cheplygina, Jianxu Chen, Evangelia Christodoulou, Beth A Cimini, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Daniel A Hashimoto, Michael M Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Jens Kleesiek, Florian Kofler, Thijs Kooi, Annette Kopp-Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern Menze, Karel G M Moons, Henning Müller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir Rajpoot, Mauricio Reyes, Michael A Riegler, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Ronald M Summers, Abdel A Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gaël Varoquaux, Ziv R Yaniv, Paul F Jäger, and Lena Maier-Hein. Understanding metric-related pitfalls in image analysis validation. Nat. Methods, 21(2):182–194, February 2024.
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, Matthew Blaschko, Florian Buettner, M. Jorge Cardoso, Jianxu Chen, Veronika Cheplygina, Evangelia Christodoulou, Beth Cimini, Gary S. Collins, Sandy Engelhardt, Keyvan Farahani, Luciana Ferrer, Adrian Galdran, Bram van Ginneken, Ben Glocker, Patrick Godau, Robert Haase, Fred Hamprecht, Daniel A. Hashimoto, Doreen Heckmann-Nötzel, Peter Hirsch, Michael M. Hoffman, Merel Huisman, Fabian Isensee, Pierre Jannin, Charles E. Kahn, Dagmar Kainmueller, Bernhard Kainz, Alexandros Karargyris, Alan Karthikesalingam, A. Emre Kavur, Hannes Kenngott, Jens Kleesiek, Andreas Kleppe, Sven Kohler, Florian Kofler, Annette Kopp-Schneider, 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, Susanne M. Rafelski, Nasir Rajpoot, Mauricio Reyes, Nicola Rieke, Michael Riegler, Hassan Rivaz, Julio Saez-Rodriguez, Clara I. Sánchez, Julien Schroeter, Anindo Saha, M. Alper Selver, Lalith Sharan, Shravya Shetty, Maarten van Smeden, Bram Stieltjes, Ronald M. Summers, Abdel A. Taha, Aleksei Tiulpin, Sotirios A. Tsaftaris, Ben Van Calster, Gaël Varoquaux, Manuel Wiesenfarth, Ziv R. Yaniv, Paul Jäger, and Lena Maier-Hein. Common limitations of image processing metrics: a picture story. 2023. arXiv:2104.05642.
Rachel M Lee, Leanna R Eisenman, Satya Khuon, Jesse S Aaron, and Teng-Leong Chew. Believing is seeing - the deceptive influence of bias in quantitative microscopy. J. Cell Sci., January 2024.
Beth A Cimini, Peter Bankhead, Rocco D'Antuono, Elnaz Fazeli, Julia Fernandez-Rodriguez, Caterina Fuster-Barceló, Robert Haase, Helena Klara Jambor, Martin L Jones, Florian Jug, Anna H Klemm, Anna Kreshuk, Stefania Marcotti, Gabriel G Martins, Sara McArdle, Kota Miura, Arrate Muñoz-Barrutia, Laura C Murphy, Michael S Nelson, Simon F Nørrelykke, Perrine Paul-Gilloteaux, Thomas Pengo, Joanna W Pylvänäinen, Lior Pytowski, Arianna Ravera, Annika Reinke, Yousr Rekik, Caterina Strambio-De-Castillia, Daniel Thédié, Virginie Uhlmann, Oliver Umney, Laura Wiggins, and Kevin W Eliceiri. The crucial role of bioimage analysts in scientific research and publication. J. Cell Sci., 137(20):jcs262322, October 2024.
Peter Bajcsy, Sreenivas Bhattiprolu, Katy Börner, Beth A Cimini, Lucy Collinson, Jan Ellenberg, Reto Fiolka, Maryellen Giger, Wojtek Goscinski, Matthew Hartley, Nathan Hotaling, Rick Horwitz, Florian Jug, Isabel Kemmer, Anna Kreshuk, Emma Lundberg, Aastha Mathur, Kedar Narayan, Shuichi Onami, Anne L Plant, Fred Prior, Jason R Swedlow, Adam Taylor, and Antje Keppler. Enabling global image data sharing in the life sciences. Nat. Methods, pages 1–5, March 2025.