Beth A Cimini (B A Cimini, Beth Cimini)

ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 117

Top Venues

Nature methods

bioRxiv : the preprint server for biology

Nature communications

Journal of microscopy

Broad Institute

University of California San Francisco (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Broad Institute

United States

Image Assay Development Team Lead :: Imaging Platform

Broad Institute

United States

Postdoctoral Fellow :: Imaging Platform

Education History

University of California San Francisco

United States

PHD :: Biochemistry and Molecular Biology

Publications

Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Hao-Feng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Y Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F Greenwald, David Van Valen, Erin Weisbart, Beth A Cimini, Trevor Cheung, Oscar Brück, Gary D Baider, Bo Wang
The multimodality cell segmentation challenge: toward universal solutions. Nature methods 21 (6) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Mariana De Niz, Rodrigo Escobedo García, Celina Terán Ramirez, Ysa Pakowski, Yuriney Abonza, Nikki Bialy, Vanessa L Orr, Andres Olivera, Victor Abonza, Karina Alleva, Silvana Allodi, Michael F Almeida, Alexis Ricardo Becerril Cuevas, Frederic Bonnet, Armando Burgos Solorio, Teng-Leong Chew, Gustavo Chiabrando, Beth A Cimini, Aurélie Cleret-Buhot, Gastón Contreras Jiménez, Laura Daza, Vanessa De Sá, Natalia De Val, Diego L Delgado-Álvarez, Kevin Eliceiri, Reto Fiolka, Hernan Grecco, Dorit Hanein, Paúl Hernández Herrera, Philip Edward Hockberger, Haydee O Hernandez, Yael Hernandez Guadarrama, Michelle S Itano, Caron A Jacobs, Luis F Jiménez-García, Vilma Jiménez Sabinina, Andres Kamaid, Antje Keppler, Abhishek Kumar, Judith Lacoste, Alenka Lovy, Kate Luby-Phelps, Anita Mahadevan-Jansen, Leonel Malacrida, Shalin B Mehta, Caroline Miller, Kildare Miranda, Joshua A Moore, Alison North, Peter O'Toole, Mariana Olivares Urbano, Lía I Pietrasanta, Rodrigo V Portugal, Andrés H Rossi, Jonathan Sanchez Contreras, Caterina Strambio-De-Castilla, Gloria Soldevila, Bruno Vale, Diana Vazquez, Chris Wood, Claire M Brown, Adan Guerrero
Building momentum through networks: Bioimaging across the Americas. Journal of microscopy 294 (3) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Julie Boucau, Threnesan Naidoo, Yuming Liu, Shatavisha Dasgupta, Neha Jain, Jennie Ruelas Castillo, Nicholas E Jacobson, Kievershen Nargan, Beth A Cimini, Kevin W Eliceiri, Adrie J C Steyn, Amy K Barczak
A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment. bioRxiv : the preprint server for biology (2024)
Beth A Cimini
Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of microscopy 295 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Beth A Cimini
Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of microscopy (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A Postdoctoral Training Program in Bioimage Analysis. bioRxiv : the preprint server for biology (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A Postdoctoral Training Program in Bioimage Analysis. bioRxiv : the preprint server for biology (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Hao-Feng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Y Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F Greenwald, David Van Valen, Erin Weisbart, Beth A Cimini, Trevor Cheung, Oscar Brück, Gary D Baider, Bo Wang
The multimodality cell segmentation challenge: toward universal solutions. Nature methods 21 (6) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Beth A Cimini
Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of microscopy (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Beth A Cimini
Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of microscopy (2024)
Srinivas Niranj Chandrasekaran, Beth A Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John G Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, Alexandr A Kalinin, John Arevalo, Marzieh Haghighi, Juan C Caicedo, Daniel Kuhn, Desiree Hernandez, James Berstler, Hamdah Shafqat-Abbasi, David E Root, Susanne E Swalley, Sakshi Garg, Shantanu Singh, Anne E Carpenter
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature methods 21 (6) (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
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, Beth A Cimini
Piximi - An Images to Discovery web tool for bioimages and beyond. bioRxiv : the preprint server for biology (2024)
Nikki Bialy, Frank Alber, Brenda J Andrews, Michael Angelo, Brian J Beliveau, Lacramioara Bintu, Alistair Nicol Boettiger, Ulrike Boehm, Claire M Brown, Mahmoud Bukar Maina, James J Chambers, Beth A Cimini, Kevin W Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N Germain, Wojtek J Goscinski, David Grünwald, Michael Halter, Dorit Hanein, John W Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A Pimentel, Anne L Plant, Andrea J Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M Spraggins, Damir Sudar, Wouter-Michiel Vierdag, Niels Volkmann, Carolina Wählby, Siyuan Steven Wang, Ziv Rafael Yaniv, Caterina Strambio-De-Castilla
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ArXiv (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Mariana De Niz, Rodrigo Escobedo García, Celina Terán Ramirez, Ysa Pakowski, Yuriney Abonza, Nikki Bialy, Vanessa L Orr, Andres Olivera, Victor Abonza, Karina Alleva, Silvana Allodi, Michael F Almeida, Alexis Ricardo Becerril Cuevas, Frederic Bonnet, Armando Burgos Solorio, Teng-Leong Chew, Gustavo Chiabrando, Beth A Cimini, Aurélie Cleret-Buhot, Gastón Contreras Jiménez, Laura Daza, Vanessa De Sá, Natalia De Val, Diego L Delgado-Álvarez, Kevin Eliceiri, Reto Fiolka, Hernan Grecco, Dorit Hanein, Paúl Hernández Herrera, Philip Edward Hockberger, Haydee O Hernandez, Yael Hernandez Guadarrama, Michelle S Itano, Caron A Jacobs, Luis F Jiménez-García, Vilma Jiménez Sabinina, Andres Kamaid, Antje Keppler, Abhishek Kumar, Judith Lacoste, Alenka Lovy, Kate Luby-Phelps, Anita Mahadevan-Jansen, Leonel Malacrida, Shalin B Mehta, Caroline Miller, Kildare Miranda, Joshua A Moore, Alison North, Peter O'Toole, Mariana Olivares Urbano, Lía I Pietrasanta, Rodrigo V Portugal, Andrés H Rossi, Jonathan Sanchez Contreras, Caterina Strambio-De-Castilla, Gloria Soldevila, Bruno Vale, Diana Vazquez, Chris Wood, Claire M Brown, Adan Guerrero
Building momentum through networks: Bioimaging across the Americas. Journal of microscopy 294 (3) (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A postdoctoral training program in bioimage analysis. Molecular biology of the cell 35 (9) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A Postdoctoral Training Program in Bioimage Analysis. bioRxiv : the preprint server for biology (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A Postdoctoral Training Program in Bioimage Analysis. bioRxiv : the preprint server for biology (2024)
Mariana De Niz, Rodrigo Escobedo García, Celina Terán Ramirez, Ysa Pakowski, Yuriney Abonza, Nikki Bialy, Vanessa L Orr, Andres Olivera, Victor Abonza, Karina Alleva, Silvana Allodi, Michael F Almeida, Alexis Ricardo Becerril Cuevas, Frederic Bonnet, Armando Burgos Solorio, Teng-Leong Chew, Gustavo Chiabrando, Beth A Cimini, Aurélie Cleret-Buhot, Gastón Contreras Jiménez, Laura Daza, Vanessa De Sá, Natalia De Val, Diego L Delgado-Álvarez, Kevin Eliceiri, Reto Fiolka, Hernan Grecco, Dorit Hanein, Paúl Hernández Herrera, Philip Edward Hockberger, Haydee O Hernandez, Yael Hernandez Guadarrama, Michelle S Itano, Caron A Jacobs, Luis F Jiménez-García, Vilma Jiménez Sabinina, Andres Kamaid, Antje Keppler, Abhishek Kumar, Judith Lacoste, Alenka Lovy, Kate Luby-Phelps, Anita Mahadevan-Jansen, Leonel Malacrida, Shalin B Mehta, Caroline Miller, Kildare Miranda, Joshua A Moore, Alison North, Peter O'Toole, Mariana Olivares Urbano, Lía I Pietrasanta, Rodrigo V Portugal, Andrés H Rossi, Jonathan Sanchez Contreras, Caterina Strambio-De-Castilla, Gloria Soldevila, Bruno Vale, Diana Vazquez, Chris Wood, Claire M Brown, Adan Guerrero
Building momentum through networks: Bioimaging across the Americas. Journal of microscopy 294 (3) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Hao-Feng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Y Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F Greenwald, David Van Valen, Erin Weisbart, Beth A Cimini, Trevor Cheung, Oscar Brück, Gary D Baider, Bo Wang
The multimodality cell segmentation challenge: toward universal solutions. Nature methods 21 (6) (2024)
Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Hao-Feng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Y Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F Greenwald, David Van Valen, Erin Weisbart, Beth A Cimini, Trevor Cheung, Oscar Brück, Gary D Baider, Bo Wang
The multimodality cell segmentation challenge: toward universal solutions. Nature methods (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods (2024)
Beth A Cimini
Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of microscopy 295 (2) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Srinivas Niranj Chandrasekaran, Beth A Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John G Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, Alexandr A Kalinin, John Arevalo, Marzieh Haghighi, Juan C Caicedo, Daniel Kuhn, Desiree Hernandez, James Berstler, Hamdah Shafqat-Abbasi, David E Root, Susanne E Swalley, Sakshi Garg, Shantanu Singh, Anne E Carpenter
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature methods (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Mariana De Niz, Rodrigo Escobedo García, Celina Terán Ramirez, Ysa Pakowski, Yuriney Abonza, Nikki Bialy, Vanessa L Orr, Andres Olivera, Victor Abonza, Karina Alleva, Silvana Allodi, Michael F Almeida, Alexis Ricardo Becerril Cuevas, Frederic Bonnet, Armando Burgos Solorio, Teng-Leong Chew, Gustavo Chiabrando, Beth A Cimini, Aurélie Cleret-Buhot, Gastón Contreras Jiménez, Laura Daza, Vanessa De Sá, Natalia De Val, Diego L Delgado-Álvarez, Kevin Eliceiri, Reto Fiolka, Hernan Grecco, Dorit Hanein, Paúl Hernández Herrera, Philip Edward Hockberger, Haydee O Hernandez, Yael Hernandez Guadarrama, Michelle S Itano, Caron A Jacobs, Luis F Jiménez-García, Vilma Jiménez Sabinina, Andres Kamaid, Antje Keppler, Abhishek Kumar, Judith Lacoste, Alenka Lovy, Kate Luby-Phelps, Anita Mahadevan-Jansen, Leonel Malacrida, Shalin B Mehta, Caroline Miller, Kildare Miranda, Joshua A Moore, Alison North, Peter O'Toole, Mariana Olivares Urbano, Lía I Pietrasanta, Rodrigo V Portugal, Andrés H Rossi, Jonathan Sanchez Contreras, Caterina Strambio-De-Castilla, Gloria Soldevila, Bruno Vale, Diana Vazquez, Chris Wood, Claire M Brown, Adan Guerrero
Building momentum through networks: Bioimaging across the Americas. Journal of microscopy 294 (3) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Hao-Feng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Y Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F Greenwald, David Van Valen, Erin Weisbart, Beth A Cimini, Trevor Cheung, Oscar Brück, Gary D Baider, Bo Wang
The multimodality cell segmentation challenge: toward universal solutions. Nature methods (2024)
Mariana De Niz, Rodrigo Escobedo García, Celina Terán Ramirez, Ysa Pakowski, Yuriney Abonza, Nikki Bialy, Vanessa L Orr, Andres Olivera, Victor Abonza, Karina Alleva, Silvana Allodi, Michael F Almeida, Alexis Ricardo Becerril Cuevas, Frederic Bonnet, Armando Burgos Solorio, Teng-Leong Chew, Gustavo Chiabrando, Beth A Cimini, Aurélie Cleret-Buhot, Gastón Contreras Jiménez, Laura Daza, Vanessa De Sá, Natalia De Val, Diego L Delgado-Álvarez, Kevin Eliceiri, Reto Fiolka, Hernan Grecco, Dorit Hanein, Paúl Hernández Herrera, Philip Edward Hockberger, Haydee O Hernandez, Yael Hernandez Guadarrama, Michelle S Itano, Caron A Jacobs, Luis F Jiménez-García, Vilma Jiménez Sabinina, Andres Kamaid, Antje Keppler, Abhishek Kumar, Judith Lacoste, Alenka Lovy, Kate Luby-Phelps, Anita Mahadevan-Jansen, Leonel Malacrida, Shalin B Mehta, Caroline Miller, Kildare Miranda, Joshua A Moore, Alison North, Peter O'Toole, Mariana Olivares Urbano, Lía I Pietrasanta, Rodrigo V Portugal, Andrés H Rossi, Jonathan Sanchez Contreras, Caterina Strambio-De-Castilla, Gloria Soldevila, Bruno Vale, Diana Vazquez, Chris Wood, Claire M Brown, Adan Guerrero
Building momentum through networks: Bioimaging across the Americas. Journal of microscopy (2024)
Fernanda Garcia-Fossa, Thaís Moraes-Lacerda, Mariana Rodrigues-da-Silva, Barbara Diaz-Rohrer, Shantanu Singh, Anne E Carpenter, Beth A Cimini, Marcelo Bispo de Jesus
Live Cell Painting: image-based profiling in live cells using Acridine Orange. bioRxiv : the preprint server for biology (2024)
Jun Ma, Ronald Xie, Shamini Ayyadhury, Cheng Ge, Anubha Gupta, Ritu Gupta, Song Gu, Yao Zhang, Gihun Lee, Joonkee Kim, Wei Lou, Hao-Feng Li, Eric Upschulte, Timo Dickscheid, José Guilherme de Almeida, Yixin Wang, Lin Han, Xin Yang, Marco Labagnara, Vojislav Gligorovski, Maxime Scheder, Sahand Jamal Rahi, Carly Kempster, Alice Y Pollitt, Leon Espinosa, Tâm Mignot, Jan Moritz Middeke, Jan-Niklas Eckardt, Wangkai Li, Zhaoyang Li, Xiaochen Cai, Bizhe Bai, Noah F Greenwald, David Van Valen, Erin Weisbart, Beth A Cimini, Trevor Cheung, Oscar Brück, Gary D Baider, Bo Wang
The multimodality cell segmentation challenge: toward universal solutions. Nature methods (2024)
Beth A Cimini
Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of microscopy 295 (2) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A Postdoctoral Training Program in Bioimage Analysis. bioRxiv : the preprint server for biology (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Srinivas Niranj Chandrasekaran, Beth A Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John G Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, Alexandr A Kalinin, John Arevalo, Marzieh Haghighi, Juan C Caicedo, Daniel Kuhn, Desiree Hernandez, James Berstler, Hamdah Shafqat-Abbasi, David E Root, Susanne E Swalley, Sakshi Garg, Shantanu Singh, Anne E Carpenter
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature methods 21 (6) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Erin Weisbart, Ankur Kumar, John Arevalo, Anne E Carpenter, Beth A Cimini, Shantanu Singh
Cell Painting Gallery: an open resource for image-based profiling. Nature methods (2024)
Srinivas Niranj Chandrasekaran, Beth A Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John G Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, Alexandr A Kalinin, John Arevalo, Marzieh Haghighi, Juan C Caicedo, Daniel Kuhn, Desiree Hernandez, James Berstler, Hamdah Shafqat-Abbasi, David E Root, Susanne E Swalley, Sakshi Garg, Shantanu Singh, Anne E Carpenter
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature methods 21 (6) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A postdoctoral training program in bioimage analysis. Molecular biology of the cell 35 (9) (2024)
Matthew Tegtmeyer, Jatin Arora, Samira Asgari, Beth A Cimini, Ajay Nadig, Emily Peirent, Dhara Liyanage, Gregory P Way, Erin Weisbart, Aparna Nathan, Tiffany Amariuta, Kevin C Eggan, Marzieh Haghighi, Steven A McCarroll, Luke O' Connor, Anne E Carpenter, Shantanu Singh, Ralda Nehme, Soumya Raychaudhuri
High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature communications 15 (1) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (2024)
Beth A Cimini, Callum Tromans-Coia, David R Stirling, Suganya Sivagurunathan, Rebecca A Senft, Pearl V Ryder, Esteban A Miglietta, Paula Llanos, Nasim Jamali, Barbara Diaz-Rohrer, Shatavisha Dasgupta, Mario Costa Cruz, Erin Weisbart, Anne E Carpenter
A postdoctoral training program in bioimage analysis. Molecular biology of the cell 35 (9) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Julie Boucau, Threnesan Naidoo, Yuming Liu, Shatavisha Dasgupta, Neha Jain, Jennie Ruelas Castillo, Nicholas E Jacobson, Kievershen Nargan, Beth A Cimini, Kevin W Eliceiri, Adrie J C Steyn, Amy K Barczak
A mouse model of TB-associated lung fibrosis reveals persistent inflammatory macrophage populations during treatment. bioRxiv : the preprint server for biology (2024)
Mariana De Niz, Rodrigo Escobedo García, Celina Terán Ramirez, Ysa Pakowski, Yuriney Abonza, Nikki Bialy, Vanessa L Orr, Andres Olivera, Victor Abonza, Karina Alleva, Silvana Allodi, Michael F Almeida, Alexis Ricardo Becerril Cuevas, Frederic Bonnet, Armando Burgos Solorio, Teng-Leong Chew, Gustavo Chiabrando, Beth A Cimini, Aurélie Cleret-Buhot, Gastón Contreras Jiménez, Laura Daza, Vanessa De Sá, Natalia De Val, Diego L Delgado-Álvarez, Kevin Eliceiri, Reto Fiolka, Hernan Grecco, Dorit Hanein, Paúl Hernández Herrera, Philip Edward Hockberger, Haydee O Hernandez, Yael Hernandez Guadarrama, Michelle S Itano, Caron A Jacobs, Luis F Jiménez-García, Vilma Jiménez Sabinina, Andres Kamaid, Antje Keppler, Abhishek Kumar, Judith Lacoste, Alenka Lovy, Kate Luby-Phelps, Anita Mahadevan-Jansen, Leonel Malacrida, Shalin B Mehta, Caroline Miller, Kildare Miranda, Joshua A Moore, Alison North, Peter O'Toole, Mariana Olivares Urbano, Lía I Pietrasanta, Rodrigo V Portugal, Andrés H Rossi, Jonathan Sanchez Contreras, Caterina Strambio-De-Castilla, Gloria Soldevila, Bruno Vale, Diana Vazquez, Chris Wood, Claire M Brown, Adan Guerrero
Building momentum through networks: Bioimaging across the Americas. Journal of microscopy 294 (3) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
Annika Reinke, Minu D Tizabi, Michael Baumgartner, Matthias Eisenmann, Doreen Heckmann-Nötzel, A Emre Kavur, Tim Rädsch, Carole H Sudre, Laura Ación, 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, Dominik T Schneider, Michal Kozubek, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Susanne M Rafelski, Nasir M 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, Gael Varoquaux, Ziv Rafael Yaniv, Paul F Jaeger, Lena Maier-Hein
Understanding metric-related pitfalls in image analysis validation. Nature methods 21 (2) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (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 Ación, Michela Antonelli, Tal Arbel, Spyridon Bakas, Arriel Benis, Matthew B Blaschko, M Jorge Cardoso, Veronika Cheplygina, Beth A Cimini, Gary Stephen 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, Dominik T Schneider, Anna Kreshuk, Tahsin Kurc, Bennett A Landman, Geert Litjens, Amin Madani, Klaus Maier-Hein, Anne L Martel, Peter Mattson, Erik Meijering, Bjoern H Menze, Karel G M Moons, Henning Muller, Brennan Nichyporuk, Felix Nickel, Jens Petersen, Nasir M Rajpoot, Nicola Rieke, Julio Saez-Rodriguez, Clara I Sánchez, Shravya Shetty, Maarten van Smeden, Ronald M Summers, Abdel Aziz Taha, Aleksei Tiulpin, Sotirios A Tsaftaris, Ben Van Calster, Gael Varoquaux, Paul F Jaeger
Metrics reloaded: recommendations for image analysis validation. Nature methods 21 (2) (2024)
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, Beth A Cimini
Piximi - An Images to Discovery web tool for bioimages and beyond. bioRxiv : the preprint server for biology (2024)
Srinivas Niranj Chandrasekaran, Beth A Cimini, Amy Goodale, Lisa Miller, Maria Kost-Alimova, Nasim Jamali, John G Doench, Briana Fritchman, Adam Skepner, Michelle Melanson, Alexandr A Kalinin, John Arevalo, Marzieh Haghighi, Juan C Caicedo, Daniel Kuhn, Desiree Hernandez, James Berstler, Hamdah Shafqat-Abbasi, David E Root, Susanne E Swalley, Sakshi Garg, Shantanu Singh, Anne E Carpenter
Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature methods 21 (6) (2024)
Nikita Moshkov, Michael Bornholdt, Santiago Benoit, Matthew Smith, Claire McQuin, Allen Goodman, Rebecca A Senft, Yu Han, Mehrtash Babadi, Peter Horvath, Beth A Cimini, Anne E Carpenter, Shantanu Singh, Juan C Caicedo
Learning representations for image-based profiling of perturbations. Nature communications 15 (1) (2024)
Josh Moore, Daniela Basurto-Lozada, Sébastien Besson, John A Bogovic, Jordao Bragantini, Jackson M Brown, Jean-Marie Burel, Xavier Casas Moreno, Gustavo de Medeiros, Erin E Diel, David Gault, Satrajit S Ghosh, Ilan Gold, Yaroslav O Halchenko, Matthew Hartley, David Horsfall, Mark S Keller, Mark Kittisopikul, Gabor Kovacs, Aybüke Küpcü Yoldaş, Koji Kyoda, Albane le Tournoulx de la Villegeorges, Tong Li, Prisca Liberali, Dominik Lindner, Melissa Linkert, Joel Lüthi, Jeremy Maitlin-Shepard, Trevor Manz, Luca Marconato, Matthew McCormick, Merlin Lange, Khaled Mohamed, William Moore, Nils Norlin, Wei Ouyang, Buğra Özdemir, Giovanni Palla, Constantin Pape, Lucas Pelkmans, Tobias Pietzsch, Stephan Preibisch, Martin Prete, Norman Rzepka, Sameeul Samee, Nicholas J Schaub, Hythem Sidky, Ahmet Can Solak, David R Stirling, Jonathan Striebel, Christian Tischer, Daniel M Toloudis, Isaac Virshup, Petr Walczysko, Alan M Watson, Erin Weisbart, Frances Wong, Kevin A Yamauchi, Omer Ali Bayraktar, Beth A Cimini, Nils Gehlenborg, Muzlifah A Haniffa, Nathan A Hotaling, Shuichi Onami, Loïc Alain Royer, Stephan Saalfeld, Oliver Stegle, Fabian Joachim Theis, Jason R Swedlow
OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochemistry and cell biology (2023)
Martin H Berryer, Gizem Rizki, Anna Nathanson, Jenny A Klein, Darina Trendafilova, Sara G Susco, Daisy Lam, Angelica Messana, Kristina M Holton, Kyle W Karhohs, Beth A Cimini, Kathleen Pfaff, Anne E Carpenter, Lee L Rubin, Lindy E Barrett
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife 12 (2023)
Nasim Jamali, Callum Tromans-Coia, Hamdah Shafqat Abbasi, Kenneth A Giuliano, Mai Hagimoto, Kevin Jan, Erika Kaneko, Stefan Letzsch, Alexander Schreiner, Jonathan Z Sexton, Mahomi Suzuki, O Joseph Trask, Mitsunari Yamaguchi, Fumiki Yanagawa, Michael Yang, Anne E Carpenter, Beth A Cimini
Assessing the performance of the Cell Painting assay across different imaging systems. bioRxiv : the preprint server for biology (2023)
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, Kevin W Eliceiri, Beth A Cimini
A biologist's guide to planning and performing quantitative bioimaging experiments. PLoS biology 21 (6) (2023)
Erin Weisbart, Callum Tromans-Coia, Barbara Diaz-Rohrer, David R Stirling, Fernanda Garcia-Fossa, Rebecca A Senft, Mark C Hiner, Marcelo B de Jesus, Kevin W Eliceiri, Beth A Cimini
CellProfiler plugins - an easy image analysis platform integration for containers and Python tools. Journal of microscopy (2023)
Martin H Berryer, Gizem Rizki, Anna Nathanson, Jenny A Klein, Darina Trendafilova, Sara G Susco, Daisy Lam, Angelica Messana, Kristina M Holton, Kyle W Karhohs, Beth A Cimini, Kathleen Pfaff, Anne E Carpenter, Lee L Rubin, Lindy E Barrett
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife 12 (2023)
Martin H Berryer, Gizem Rizki, Anna Nathanson, Jenny A Klein, Darina Trendafilova, Sara G Susco, Daisy Lam, Angelica Messana, Kristina M Holton, Kyle W Karhohs, Beth A Cimini, Kathleen Pfaff, Anne E Carpenter, Lee L Rubin, Lindy E Barrett
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife 12 (2023)
Martin H Berryer, Gizem Rizki, Anna Nathanson, Jenny A Klein, Darina Trendafilova, Sara G Susco, Daisy Lam, Angelica Messana, Kristina M Holton, Kyle W Karhohs, Beth A Cimini, Kathleen Pfaff, Anne E Carpenter, Lee L Rubin, Lindy E Barrett
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife 12 (2023)
Meraj Ramezani, Julia R Bauman, Avtar Singh, Erin Weisbart, John Yong, Maria Lozada, Gregory P Way, Sanam L Kavari, Celeste Diaz, Marzieh Haghighi, Thiago Martins Batista, Joaquín Pérez-Schindler, Melina Claussnitzer, Shantanu Singh, Beth A Cimini, Paul C Blainey, Anne E Carpenter, Calvin H Jan, James T Neal
A genome-wide atlas of human cell morphology. bioRxiv : the preprint server for biology (2023)
Suganya Sivagurunathan, Stefania Marcotti, Carl J Nelson, Martin L Jones, David J Barry, Thomas J A Slater, Kevin W Eliceiri, Beth A Cimini
Bridging Imaging Users to Imaging Analysis - A community survey. Journal of microscopy (2023)
Martin H Berryer, Gizem Rizki, Anna Nathanson, Jenny A Klein, Darina Trendafilova, Sara G Susco, Daisy Lam, Angelica Messana, Kristina M Holton, Kyle W Karhohs, Beth A Cimini, Kathleen Pfaff, Anne E Carpenter, Lee L Rubin, Lindy E Barrett
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife 12 (2023)
Jessica Lacoste, Marzieh Haghighi, Shahan Haider, Zhen-Yuan Lin, Dmitri Segal, Chloe Reno, Wesley Wei Qian, Xueting Xiong, Hamdah Shafqat Abbasi, Pearl V Ryder, Rebecca A Senft, Beth A Cimini, Frederick P Roth, Michael S Calderwood, David Hill, Marc Vidal, S Stephen Yi, Nidhi Sahni, Jian Peng, Anne-Claude Gingras, Shantanu Singh, Anne E Carpenter, Mikko Taipale
Pervasive mislocalization of pathogenic coding variants underlying human disorders. bioRxiv : the preprint server for biology (2023)
Erin Weisbart, Beth A Cimini
Distributed-Something: scripts to leverage AWS storage and computing for distributed workflows at scale. Nature methods (2023)
Christopher Schmied, Michael S Nelson, Sergiy V 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 C Ecker, Kevin W Eliceiri, Julia Fernandez-Rodriguez, Nathalie Gaudreault, Laurent Gelman, David Grünwald, Tingting Gu, Nadia Halidi, Mathias Hammer, Matthew Hartley, Marie Held, Florian Jug, Varun Kapoor, Ayse Aslihan Koksoy, Judith Lacoste, Sylvia E 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 L 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-Castilla, Douglas J Taatjes, Christian Tischer, Helena Klara Jambor
Community-developed checklists for publishing images and image analyses. Nature methods (2023)
Megan E Kelley, Adi Y Berman, David R Stirling, Beth A Cimini, Yu Han, Shantanu Singh, Anne E Carpenter, Tarun M Kapoor, Gregory P Way
High-content microscopy reveals a morphological signature of bortezomib resistance. bioRxiv : the preprint server for biology (2023)
Nasim Jamali, Callum Tromans-Coia, Hamdah Shafqat Abbasi, Kenneth A Giuliano, Mai Hagimoto, Kevin Jan, Erika Kaneko, Stefan Letzsch, Alexander Schreiner, Jonathan Z Sexton, Mahomi Suzuki, O Joseph Trask, Mitsunari Yamaguchi, Fumiki Yanagawa, Michael Yang, Anne E Carpenter, Beth A Cimini
Assessing the performance of the Cell Painting assay across different imaging systems. bioRxiv : the preprint server for biology (2023)
Viktoria Glunk, Samantha Laber, Nasa Sinnott-Armstrong, Débora R Sobreira, Sophie M Strobel, Thiago Martins Batista, Phil Kubitz, Bahareh Nemati Moud, Hannah Ebert, Yi Huang, Beate Brandl, Garrett Garborcauskas, Julius Honecker, David R Stirling, Nezar Abdennur, Virtu Calabuig-Navarro, Thomas Skurk, Soeren Ocvirk, Kerstin Stemmer, Beth A Cimini, Anne E Carpenter, Simon Nitter Dankel, Cecilia M Lindgren, Hans Hauner, Marcelo Aguiar Nobrega, Melina Claussnitzer
A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nature metabolism 5 (5) (2023)
Callum Tromans-Coia, Nasim Jamali, Hamdah Shafqat Abbasi, Kenneth A Giuliano, Mai Hagimoto, Kevin Jan, Erika Kaneko, Stefan Letzsch, Alexander Schreiner, Jonathan Z Sexton, Mahomi Suzuki, O Joseph Trask, Mitsunari Yamaguchi, Fumiki Yanagawa, Michael Yang, Anne E Carpenter, Beth A Cimini
Assessing the performance of the Cell Painting assay across different imaging systems. Cytometry. Part A : the journal of the International Society for Analytical Cytology (2023)
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, Kevin W Eliceiri, Beth A Cimini
A biologist's guide to planning and performing quantitative bioimaging experiments. PLoS biology 21 (6) (2023)
Martin H Berryer, Gizem Rizki, Anna Nathanson, Jenny A Klein, Darina Trendafilova, Sara G Susco, Daisy Lam, Angelica Messana, Kristina M Holton, Kyle W Karhohs, Beth A Cimini, Kathleen Pfaff, Anne E Carpenter, Lee L Rubin, Lindy E Barrett
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife 12 (2023)
Martin H Berryer, Gizem Rizki, Anna Nathanson, Jenny A Klein, Darina Trendafilova, Sara G Susco, Daisy Lam, Angelica Messana, Kristina M Holton, Kyle W Karhohs, Beth A Cimini, Kathleen Pfaff, Anne E Carpenter, Lee L Rubin, Lindy E Barrett
High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife 12 (2023)
Megan E Kelley, Adi Y Berman, David R Stirling, Beth A Cimini, Yu Han, Shantanu Singh, Anne E Carpenter, Tarun M Kapoor, Gregory P Way
High-content microscopy reveals a morphological signature of bortezomib resistance. bioRxiv : the preprint server for biology (2023)
Anne E Carpenter, Beth A Cimini, Kevin W Eliceiri
Smart microscopes of the future. Nature methods 20 (7) (2023)

Beth A Cimini.css-eqlu8i{font-size:small;padding-left:4px;} (B A Cimini, Beth Cimini)

Publication Activity (10 Years)

Top Topics

Top Venues

Beth A Cimini (B A Cimini, Beth Cimini)