Broad Institute
Beth Cimini
415 Main Street
Cambridge, MA 02142
https://www.broadinstitute.org/imaging
RRID: RRID:SCR_024653
Bioimage Informatics
Image Data Management
Image Processing And Analysis
1.) Tromans-Coia C, Jamali N, Abbasi HS, Giuliano KA, Hagimoto M, Jan K, Kaneko E, Letzsch S, Schreiner A, Sexton JZ, Suzuki M, Trask OJ, Yamaguchi M, Yanagawa F, Yang M, Carpenter AE, Cimini BA (2023 Oct 3). Assessing the performance of the Cell Painting assay across different imaging systems. Cytometry. Part A : the journal of the International Society for Analytical Cytology, (), . doi: 10.1002/cyto.a.24786. ID: 37789738.
2.) Kelley ME, Berman AY, Stirling DR, Cimini BA, Han Y, Singh S, Carpenter AE, Kapoor TM, Way GP (2023 Sep 27). High-content microscopy reveals a morphological signature of bortezomib resistance. eLife, 12(), . . ID: 37753907.
3.) Schmied C, Nelson MS, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho MT, Chiritescu C, Christopher J, Cimini BA, Conde-Sousa E, Ebner M, Ecker R, Eliceiri K, Fernandez-Rodriguez J, Gaudreault N, Gelman L, Grunwald D, Gu T, Halidi N, Hammer M, Hartley M, Held M, Jug F, Kapoor V, Koksoy AA, Lacoste J, Le Dévédec S, Le Guyader S, Liu P, Martins GG, Mathur A, Miura K, Montero Llopis P, Nitschke R, North A, Parslow AC, Payne-Dwyer A, Plantard L, Ali R, Schroth-Diez B, Schüt (2023 Sep 14). Community-developed checklists for publishing images and image analyses. Nature methods, (), . doi: 10.1038/s41592-023-01987-9. ID: 37710020.
4.) Weisbart E, Tromans-Coia C, Diaz-Rohrer B, Stirling DR, Garcia-Fossa F, Senft RA, Hiner MC, de Jesus MB, Eliceiri KW, Cimini BA (2023 Sep 10). CellProfiler plugins - An easy image analysis platform integration for containers and Python tools. Journal of microscopy, (), . doi: 10.1111/jmi.13223. ID: 37690102.
5.) Lacoste J, Haghighi M, Haider S, Lin ZY, Segal D, Reno C, Qian WW, Xiong X, Shafqat-Abbasi H, Ryder PV, Senft R, Cimini BA, Roth FP, Calderwood M, Hill D, Vidal M, Yi SS, Sahni N, Peng J, Gingras AC, Singh S, Carpenter AE, Taipale M (2023 Sep 5). Pervasive mislocalization of pathogenic coding variants underlying human disorders. bioRxiv : the preprint server for biology, (), . . ID: 37732209.
6.) Ramezani M, Bauman J, Singh A, Weisbart E, Yong J, Lozada M, Way GP, Kavari SL, Diaz C, Haghighi M, Batista TM, Pérez-Schindler J, Claussnitzer M, Singh S, Cimini BA, Blainey PC, Carpenter AE, Jan CH, Neal JT (2023 Aug 7). A genome-wide atlas of human cell morphology. bioRxiv : the preprint server for biology, (), . . ID: 37609130.
7.) Cimini BA, Eliceiri KW (2023 Jul). The Twenty Questions of bioimage object analysis. Nature methods, 20(7), 976-978. . ID: 37434006.
8.) Glunk V, Laber S, Sinnott-Armstrong N, Sobreira DR, Strobel SM, Batista TM, Kubitz P, Moud BN, Ebert H, Huang Y, Brandl B, Garbo G, Honecker J, Stirling DR, Abdennur N, Calabuig-Navarro V, Skurk T, Ocvirk S, Stemmer K, Cimini BA, Carpenter AE, Dankel SN, Lindgren CM, Hauner H, Nobrega MA, Claussnitzer M (2023 May). A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nature metabolism, 5(5), 861-879. doi: 10.1038/s42255-023-00807-w. ID: 37253881.
9.) Berryer MH, Rizki G, Nathanson A, Klein JA, Trendafilova D, Susco SG, Lam D, Messana A, Holton KM, Karhohs KW, Cimini BA, Pfaff K, Carpenter AE, Rubin LL, Barrett LE (2023 Apr 21). High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. eLife, 12(), . . ID: 37083703.
The Broad Institute Imaging Platform (https://www.broadinstitute.org/imaging) helps users turn images into answers by offering assistance and training with open source image analysis tools, creating custom image analysis workflows, and even creating custom software for image analysis when needed. We are open to collaboration with academics, non-profits, and for-profit organizations.
