CellProfiler 3.0: Next-generation image processing for biology
McQuin, Claire, Goodman, Allen, Chernyshev, Vasiliy, Kamentsky, Lee, Cimini, Beth A, Karhohs, Kyle W, Doan, Minh, Ding, Liya, Rafelski, Susanne M, Thirstrup, Derek, Wiegraebe, Winfried, Singh, Shantanu, Becker, Tim, Caicedo, Juan C, Carpenter, Anne E
Published in PLoS biology (03.07.2018)
Published in PLoS biology (03.07.2018)
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Journal Article
CellProfiler 4: improvements in speed, utility and usability
Stirling, David R, Swain-Bowden, Madison J, Lucas, Alice M, Carpenter, Anne E, Cimini, Beth A, Goodman, Allen
Published in BMC bioinformatics (10.09.2021)
Published in BMC bioinformatics (10.09.2021)
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Journal Article
Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System
Chen, Baohui, Gilbert, Luke A., Cimini, Beth A., Schnitzbauer, Joerg, Zhang, Wei, Li, Gene-Wei, Park, Jason, Blackburn, Elizabeth H., Weissman, Jonathan S., Qi, Lei S., Huang, Bo
Published in Cell (19.12.2013)
Published in Cell (19.12.2013)
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Journal Article
CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis
Stirling, David R, Carpenter, Anne E, Cimini, Beth A
Published in Bioinformatics (Oxford, England) (05.11.2021)
Published in Bioinformatics (Oxford, England) (05.11.2021)
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Journal Article
Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
Caicedo, Juan C., Goodman, Allen, Karhohs, Kyle W., Cimini, Beth A., Ackerman, Jeanelle, Haghighi, Marzieh, Heng, CherKeng, Becker, Tim, Doan, Minh, McQuin, Claire, Rohban, Mohammad, Singh, Shantanu, Carpenter, Anne E.
Published in Nature methods (01.12.2019)
Published in Nature methods (01.12.2019)
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Journal Article
Metrics reloaded: recommendations for image analysis validation
Maier-Hein, Lena, Reinke, Annika, Godau, Patrick, Tizabi, Minu D., Buettner, Florian, Christodoulou, Evangelia, Glocker, Ben, Isensee, Fabian, Kleesiek, Jens, Kozubek, Michal, Reyes, Mauricio, Riegler, Michael A., Wiesenfarth, Manuel, Kavur, A. Emre, Sudre, Carole H., Baumgartner, Michael, Eisenmann, Matthias, Heckmann-Nötzel, Doreen, Rädsch, Tim, Acion, Laura, Antonelli, Michela, Arbel, Tal, Bakas, Spyridon, Benis, Arriel, Blaschko, Matthew B., Cardoso, M. Jorge, Cheplygina, Veronika, Cimini, Beth A., Collins, Gary S., Farahani, Keyvan, Ferrer, Luciana, Galdran, Adrian, van Ginneken, Bram, Haase, Robert, Hashimoto, Daniel A., Hoffman, Michael M., Huisman, Merel, Jannin, Pierre, Kahn, Charles E., Kainmueller, Dagmar, Kainz, Bernhard, Karargyris, Alexandros, Karthikesalingam, Alan, Kofler, Florian, Kopp-Schneider, Annette, Kreshuk, Anna, Kurc, Tahsin, Landman, Bennett A., Litjens, Geert, Madani, Amin, Maier-Hein, Klaus, Martel, Anne L., Mattson, Peter, Meijering, Erik, Menze, Bjoern, Moons, Karel G. M., Müller, Henning, Nichyporuk, Brennan, Nickel, Felix, Petersen, Jens, Rajpoot, Nasir, Rieke, Nicola, Saez-Rodriguez, Julio, Sánchez, Clara I., Shetty, Shravya, van Smeden, Maarten, Summers, Ronald M., Taha, Abdel A., Tiulpin, Aleksei, Tsaftaris, Sotirios A., Van Calster, Ben, Varoquaux, Gaël, Jäger, Paul F.
Published in Nature methods (01.02.2024)
Published in Nature methods (01.02.2024)
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Journal Article
Open-source deep-learning software for bioimage segmentation
Lucas, Alice M, Ryder, Pearl V, Li, Bin, Cimini, Beth A, Eliceiri, Kevin W, Carpenter, Anne E
Published in Molecular biology of the cell (19.04.2021)
Published in Molecular biology of the cell (19.04.2021)
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Journal Article
Cell Painting Gallery: an open resource for image-based profiling
Weisbart, Erin, Kumar, Ankur, Arevalo, John, Carpenter, Anne E., Cimini, Beth A., Singh, Shantanu
Published in Nature methods (01.10.2024)
Published in Nature methods (01.10.2024)
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Journal Article
Genetic and transcriptional evolution alters cancer cell line drug response
Ben-David, Uri, Siranosian, Benjamin, Ha, Gavin, Tang, Helen, Oren, Yaara, Hinohara, Kunihiko, Strathdee, Craig A., Dempster, Joshua, Lyons, Nicholas J., Burns, Robert, Nag, Anwesha, Kugener, Guillaume, Cimini, Beth, Tsvetkov, Peter, Maruvka, Yosef E., O’Rourke, Ryan, Garrity, Anthony, Tubelli, Andrew A., Bandopadhayay, Pratiti, Tsherniak, Aviad, Vazquez, Francisca, Wong, Bang, Birger, Chet, Ghandi, Mahmoud, Thorner, Aaron R., Bittker, Joshua A., Meyerson, Matthew, Getz, Gad, Beroukhim, Rameen, Golub, Todd R.
Published in Nature (London) (01.08.2018)
Published in Nature (London) (01.08.2018)
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Journal Article
A biologist's guide to planning and performing quantitative bioimaging experiments
Senft, Rebecca A, Diaz-Rohrer, Barbara, Colarusso, Pina, Swift, Lucy, Jamali, Nasim, Jambor, Helena, Pengo, Thomas, Brideau, Craig, Llopis, Paula Montero, Uhlmann, Virginie, Kirk, Jason, Gonzales, Kevin Andrew, Bankhead, Peter, Evans, 3rd, Edward L, Eliceiri, Kevin W, Cimini, Beth A
Published in PLoS biology (27.06.2023)
Published in PLoS biology (27.06.2023)
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Journal Article
Scientific Community Image Forum: A discussion forum for scientific image software
Rueden, Curtis T, Ackerman, Jeanelle, Arena, Ellen T, Eglinger, Jan, Cimini, Beth A, Goodman, Allen, Carpenter, Anne E, Eliceiri, Kevin W
Published in PLoS biology (19.06.2019)
Published in PLoS biology (19.06.2019)
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Journal Article
The multimodality cell segmentation challenge: toward universal solutions
Ma, Jun, Xie, Ronald, Ayyadhury, Shamini, Ge, Cheng, Gupta, Anubha, Gupta, Ritu, Gu, Song, Zhang, Yao, Lee, Gihun, Kim, Joonkee, Lou, Wei, Li, Haofeng, Upschulte, Eric, Dickscheid, Timo, de Almeida, José Guilherme, Wang, Yixin, Han, Lin, Yang, Xin, Labagnara, Marco, Gligorovski, Vojislav, Scheder, Maxime, Rahi, Sahand Jamal, Kempster, Carly, Pollitt, Alice, Espinosa, Leon, Mignot, Tâm, Middeke, Jan Moritz, Eckardt, Jan-Niklas, Li, Wangkai, Li, Zhaoyang, Cai, Xiaochen, Bai, Bizhe, Greenwald, Noah F., Van Valen, David, Weisbart, Erin, Cimini, Beth A., Cheung, Trevor, Brück, Oscar, Bader, Gary D., Wang, Bo
Published in Nature methods (01.06.2024)
Published in Nature methods (01.06.2024)
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Journal Article
Visualization of actin filaments and monomers in somatic cell nuclei
Belin, Brittany J, Cimini, Beth A, Blackburn, Elizabeth H, Mullins, R Dyche
Published in Molecular biology of the cell (01.04.2013)
Published in Molecular biology of the cell (01.04.2013)
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