| Year |
Citation |
Score |
| 2024 |
Garcia-Fossa F, Moraes-Lacerda T, Rodrigues-da-Silva M, Diaz-Rohrer B, Singh S, Carpenter AE, Cimini BA, de Jesus MB. Live Cell Painting: image-based profiling in live cells using Acridine Orange. Biorxiv : the Preprint Server For Biology. PMID 39257795 DOI: 10.1101/2024.08.28.610144 |
0.376 |
|
| 2024 |
Weisbart E, Kumar A, Arevalo J, Carpenter AE, Cimini BA, Singh S. Cell Painting Gallery: an open resource for image-based profiling. Nature Methods. PMID 39223397 DOI: 10.1038/s41592-024-02399-z |
0.768 |
|
| 2024 |
Cimini BA, Tromans-Coia C, Stirling DR, Sivagurunathan S, Senft RA, Ryder PV, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz M, Weisbart E, Carpenter AE. A postdoctoral training program in bioimage analysis. Molecular Biology of the Cell. 35: pe2. PMID 39105698 DOI: 10.1091/mbc.E24-05-0214 |
0.436 |
|
| 2024 |
Riendeau JM, Gillette AA, Guzman EC, Cruz MC, Kralovec A, Udgata S, Schmitz A, Deming DA, Cimini BA, Skala MC. Cellpose as a reliable method for single-cell segmentation of autofluorescence microscopy images. Biorxiv : the Preprint Server For Biology. PMID 38915614 DOI: 10.1101/2024.06.07.597994 |
0.405 |
|
| 2024 |
Moser LM, Gogoberidze N, Papaleo A, Lucas A, Dao D, Friedrich CA, Paavolainen L, Molnar C, Stirling DR, Hung J, Wang R, Tromans-Coia C, Li B, Evans EL, Eliceiri KW, ... ... Cimini BA, et al. Piximi - An Images to Discovery web tool for bioimages and beyond. Biorxiv : the Preprint Server For Biology. PMID 38895349 DOI: 10.1101/2024.06.03.597232 |
0.612 |
|
| 2024 |
Cimini BA, Tromans-Coia C, Stirling D, Sivagurunathan S, Senft R, Ryder P, Miglietta E, Llanos P, Jamali N, Diaz-Rohrer B, Dasgupta S, Cruz M, Weisbart E, Carpenter AE. A Postdoctoral Training Program in Bioimage Analysis. Biorxiv : the Preprint Server For Biology. PMID 38798545 DOI: 10.1101/2024.05.13.593910 |
0.436 |
|
| 2024 |
Chandrasekaran SN, Cimini BA, Goodale A, Miller L, Kost-Alimova M, Jamali N, Doench JG, Fritchman B, Skepner A, Melanson M, Kalinin AA, Arevalo J, Haghighi M, Caicedo JC, Kuhn D, et al. Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations. Nature Methods. PMID 38594452 DOI: 10.1038/s41592-024-02241-6 |
0.747 |
|
| 2024 |
Cimini BA. Creating and troubleshooting microscopy analysis workflows: Common challenges and common solutions. Journal of Microscopy. PMID 38532662 DOI: 10.1111/jmi.13288 |
0.415 |
|
| 2024 |
Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, ... ... Cimini BA, et al. The multimodality cell segmentation challenge: toward universal solutions. Nature Methods. PMID 38532015 DOI: 10.1038/s41592-024-02233-6 |
0.443 |
|
| 2024 |
Cimini BA. Creating and troubleshooting microscopy analysis workflows: common challenges and common solutions. Arxiv. PMID 38495561 |
0.414 |
|
| 2024 |
Moshkov N, Bornholdt M, Benoit S, Smith M, McQuin C, Goodman A, Senft RA, Han Y, Babadi M, Horvath P, Cimini BA, Carpenter AE, Singh S, Caicedo JC. Learning representations for image-based profiling of perturbations. Nature Communications. 15: 1594. PMID 38383513 DOI: 10.1038/s41467-024-45999-1 |
0.76 |
|
| 2024 |
Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, et al. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data. Arxiv. PMID 38351940 |
0.394 |
|
| 2024 |
Weisbart E, Kumar A, Arevalo J, Carpenter AE, Cimini BA, Singh S. Cell Painting Gallery: an open resource for image-based profiling. Arxiv. PMID 38351939 |
0.768 |
|
| 2024 |
Maier-Hein L, Reinke A, Godau P, Tizabi MD, Buettner F, Christodoulou E, Glocker B, Isensee F, Kleesiek J, Kozubek M, Reyes M, Riegler MA, Wiesenfarth M, Kavur AE, Sudre CH, ... ... Cimini BA, et al. Metrics reloaded: recommendations for image analysis validation. Nature Methods. 21: 195-212. PMID 38347141 DOI: 10.1038/s41592-023-02151-z |
0.304 |
|
| 2024 |
Reinke A, Tizabi MD, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Kavur AE, Rädsch T, Sudre CH, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Buettner F, Cardoso MJ, ... ... Cimini BA, et al. Understanding metric-related pitfalls in image analysis validation. Nature Methods. 21: 182-194. PMID 38347140 DOI: 10.1038/s41592-023-02150-0 |
0.377 |
|
| 2024 |
Tegtmeyer M, Arora J, Asgari S, Cimini BA, Nadig A, Peirent E, Liyanage D, Way GP, Weisbart E, Nathan A, Amariuta T, Eggan K, Haghighi M, McCarroll SA, O'Connor L, et al. High-dimensional phenotyping to define the genetic basis of cellular morphology. Nature Communications. 15: 347. PMID 38184653 DOI: 10.1038/s41467-023-44045-w |
0.788 |
|
| 2023 |
Gogoberidze N, Cimini BA. Defining the boundaries: challenges and advances in identifying cells in microscopy images. Current Opinion in Biotechnology. 85: 103055. PMID 38142646 DOI: 10.1016/j.copbio.2023.103055 |
0.392 |
|
| 2023 |
Serrano E, Chandrasekaran SN, Bunten D, Brewer KI, Tomkinson J, Kern R, Bornholdt M, Fleming S, Pei R, Arevalo J, Tsang H, Rubinetti V, Tromans-Coia C, Becker T, Weisbart E, ... ... Cimini BA, et al. Reproducible image-based profiling with Pycytominer. Arxiv. PMID 38045474 |
0.784 |
|
| 2023 |
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, ... ... Cimini BA, et al. Assessing the performance of the Cell Painting assay across different imaging systems. Cytometry. Part a : the Journal of the International Society For Analytical Cytology. PMID 37789738 DOI: 10.1002/cyto.a.24786 |
0.812 |
|
| 2023 |
Kelley ME, Berman AY, Stirling DR, Cimini BA, Han Y, Singh S, Carpenter AE, Kapoor TM, Way GP. High-content microscopy reveals a morphological signature of bortezomib resistance. Elife. 12. PMID 37753907 DOI: 10.7554/eLife.91362 |
0.761 |
|
| 2023 |
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, et al. Pervasive mislocalization of pathogenic coding variants underlying human disorders. Biorxiv : the Preprint Server For Biology. PMID 37732209 DOI: 10.1101/2023.09.05.556368 |
0.671 |
|
| 2023 |
Sivagurunathan S, Marcotti S, Nelson CJ, Jones ML, Barry DJ, Slater TJA, Eliceiri KW, Cimini BA. Bridging Imaging Users to Imaging Analysis - A community survey. Journal of Microscopy. PMID 37727897 DOI: 10.1111/jmi.13229 |
0.404 |
|
| 2023 |
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, et al. Community-developed checklists for publishing images and image analyses. Nature Methods. PMID 37710020 DOI: 10.1038/s41592-023-01987-9 |
0.432 |
|
| 2023 |
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, et al. A genome-wide atlas of human cell morphology. Biorxiv : the Preprint Server For Biology. PMID 37609130 DOI: 10.1101/2023.08.06.552164 |
0.79 |
|
| 2023 |
Ouyang W, Eliceiri KW, Cimini BA. Moving beyond the desktop: prospects for practical bioimage analysis via the web. Frontiers in Bioinformatics. 3: 1233748. PMID 37560357 DOI: 10.3389/fbinf.2023.1233748 |
0.313 |
|
| 2023 |
Laber S, Strobel S, Mercader JM, Dashti H, Dos Santos FRC, Kubitz P, Jackson M, Ainbinder A, Honecker J, Agrawal S, Garborcauskas G, Stirling DR, Leong A, Figueroa K, Sinnott-Armstrong N, ... ... Cimini BA, et al. Discovering cellular programs of intrinsic and extrinsic drivers of metabolic traits using LipocyteProfiler. Cell Genomics. 3: 100346. PMID 37492099 DOI: 10.1016/j.xgen.2023.100346 |
0.747 |
|
| 2023 |
Carpenter AE, Cimini BA, Eliceiri KW. Smart microscopes of the future. Nature Methods. 20: 962-964. PMID 37434001 DOI: 10.1038/s41592-023-01912-0 |
0.461 |
|
| 2023 |
Senft RA, Diaz-Rohrer B, Colarusso P, Swift L, Jamali N, Jambor H, Pengo T, Brideau C, Llopis PM, Uhlmann V, Kirk J, Gonzales KA, Bankhead P, Evans EL, Eliceiri KW, ... Cimini BA, et al. A biologist's guide to planning and performing quantitative bioimaging experiments. Plos Biology. 21: e3002167. PMID 37368874 DOI: 10.1371/journal.pbio.3002167 |
0.339 |
|
| 2023 |
Cimini BA, Chandrasekaran SN, Kost-Alimova M, Miller L, Goodale A, Fritchman B, Byrne P, Garg S, Jamali N, Logan DJ, Concannon JB, Lardeau CH, Mouchet E, Singh S, Shafqat Abbasi H, et al. Optimizing the Cell Painting assay for image-based profiling. Nature Protocols. PMID 37344608 DOI: 10.1038/s41596-023-00840-9 |
0.769 |
|
| 2023 |
Sivagurunathan S, Marcotti S, Nelson CJ, Jones ML, Barry DJ, Slater TJA, Eliceiri KW, Cimini BA. Bridging Imaging Users to Imaging Analysis - A community survey. Biorxiv : the Preprint Server For Biology. PMID 37333353 DOI: 10.1101/2023.06.05.543701 |
0.401 |
|
| 2023 |
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, ... ... Cimini BA, et al. A non-coding variant linked to metabolic obesity with normal weight affects actin remodelling in subcutaneous adipocytes. Nature Metabolism. 5: 861-879. PMID 37253881 DOI: 10.1038/s42255-023-00807-w |
0.483 |
|
| 2023 |
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. High-content synaptic phenotyping in human cellular models reveals a role for BET proteins in synapse assembly. Elife. 12. PMID 37083703 DOI: 10.7554/eLife.80168 |
0.763 |
|
| 2023 |
Reinke A, Tizabi MD, Baumgartner M, Eisenmann M, Heckmann-Nötzel D, Kavur AE, Rädsch T, Sudre CH, Acion L, Antonelli M, Arbel T, Bakas S, Benis A, Blaschko M, Büttner F, ... ... Cimini BA, et al. Understanding metric-related pitfalls in image analysis validation. Arxiv. PMID 36945687 |
0.343 |
|
| 2023 |
Volpe G, Wählby C, Tian L, Hecht M, Yakimovich A, Monakhova K, Waller L, Sbalzarini IF, Metzler CA, Xie M, Zhang K, Lenton ICD, Rubinsztein-Dunlop H, Brunner D, Bai B, ... ... Cimini BA, et al. Roadmap on Deep Learning for Microscopy. Arxiv. PMID 36945686 |
0.327 |
|
| 2023 |
Garcia-Fossa F, Cruz MC, Haghighi M, de Jesus MB, Singh S, Carpenter AE, Cimini BA. Interpreting Image-based Profiles using Similarity Clustering and Single-Cell Visualization. Current Protocols. 3: e713. PMID 36921124 DOI: 10.1002/cpz1.713 |
0.76 |
|
| 2023 |
Jamali N, Tromans-Coia C, 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, ... ... Cimini BA, et al. Assessing the performance of the Cell Painting assay across different imaging systems. Biorxiv : the Preprint Server For Biology. PMID 36824835 DOI: 10.1101/2023.02.15.528711 |
0.812 |
|
| 2023 |
Schmied C, Nelson M, Avilov S, Bakker GJ, Bertocchi C, Bischof J, Boehm U, Brocher J, Carvalho M, Chiritescu C, Christopher J, Cimini B, Conde-Sousa E, Ebner M, Ecker R, et al. Community-developed checklists for publishing images and image analysis. Arxiv. PMID 36824427 |
0.431 |
|
| 2022 |
Way GP, Natoli T, Adeboye A, Litichevskiy L, Yang A, Lu X, Caicedo JC, Cimini BA, Karhohs K, Logan DJ, Rohban MH, Kost-Alimova M, Hartland K, Bornholdt M, Chandrasekaran SN, et al. Morphology and gene expression profiling provide complementary information for mapping cell state. Cell Systems. 13: 911-923.e9. PMID 36395727 DOI: 10.1016/j.cels.2022.10.001 |
0.763 |
|
| 2022 |
Haghighi M, Caicedo JC, Cimini BA, Carpenter AE, Singh S. High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations. Nature Methods. PMID 36344834 DOI: 10.1038/s41592-022-01667-0 |
0.722 |
|
| 2022 |
Rueden CT, Hiner MC, Evans EL, Pinkert MA, Lucas AM, Carpenter AE, Cimini BA, Eliceiri KW. PyImageJ: A library for integrating ImageJ and Python. Nature Methods. PMID 36253645 DOI: 10.1038/s41592-022-01655-4 |
0.432 |
|
| 2021 |
Jamali N, Dobson ET, Eliceiri KW, Carpenter AE, Cimini BA. 2020 BioImage Analysis Survey: Community experiences and needs for the future. Biological Imaging. 1. PMID 35387317 DOI: 10.1017/S2633903X21000039 |
0.579 |
|
| 2021 |
Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A. CellProfiler 4: improvements in speed, utility and usability. Bmc Bioinformatics. 22: 433. PMID 34507520 DOI: 10.1186/s12859-021-04344-9 |
0.647 |
|
| 2021 |
Stirling DR, Carpenter AE, Cimini BA. CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. Bioinformatics (Oxford, England). PMID 34478488 DOI: 10.1093/bioinformatics/btab634 |
0.569 |
|
| 2021 |
Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Communications Biology. 4: 786. PMID 34168275 DOI: 10.1038/s42003-021-02276-x |
0.784 |
|
| 2021 |
Dobson ETA, Cimini B, Klemm AH, Wählby C, Carpenter AE, Eliceiri KW. ImageJ and CellProfiler: Complements in Open-Source Bioimage Analysis. Current Protocols. 1: e89. PMID 34038030 DOI: 10.1002/cpz1.89 |
0.655 |
|
| 2021 |
Lucas AM, Ryder PV, Li B, Cimini BA, Eliceiri KW, Carpenter AE. Open-source deep-learning software for bioimage segmentation. Molecular Biology of the Cell. 32: 823-829. PMID 33872058 DOI: 10.1091/mbc.E20-10-0660 |
0.577 |
|
| 2020 |
Danielson E, Perez de Arce K, Cimini B, Wamhoff EC, Singh S, Cottrell JR, Carpenter AE, Bathe M. Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging. Eneuro. PMID 33355295 DOI: 10.1523/ENEURO.0286-20.2020 |
0.669 |
|
| 2020 |
Caicedo JC, Goodman A, Karhohs KW, Cimini BA, Ackerman J, Haghighi M, Heng C, Becker T, Doan M, McQuin C, Rohban M, Singh S, Carpenter AE. Publisher Correction: Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods. PMID 31969730 DOI: 10.1038/S41592-020-0733-Z |
0.751 |
|
| 2019 |
Caicedo JC, Goodman A, Karhohs KW, Cimini BA, Ackerman J, Haghighi M, Heng C, Becker T, Doan M, McQuin C, Rohban M, Singh S, Carpenter AE. Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl. Nature Methods. PMID 31636459 DOI: 10.1038/S41592-019-0612-7 |
0.787 |
|
| 2019 |
Rueden CT, Ackerman J, Arena ET, Eglinger J, Cimini BA, Goodman A, Carpenter AE, Eliceiri KW. Scientific Community Image Forum: A discussion forum for scientific image software. Plos Biology. 17: e3000340. PMID 31216269 DOI: 10.1371/Journal.Pbio.3000340 |
0.594 |
|
| 2018 |
McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE. CellProfiler 3.0: Next-generation image processing for biology. Plos Biology. 16: e2005970. PMID 29969450 DOI: 10.1371/Journal.Pbio.2005970 |
0.782 |
|
| 2016 |
Thorvaldsdottir B, Cimini BA, Diolaiti ME, Aradottir M, Olafsdottir K, Jonasson JG, Blackburn EH, Eyfjörd JE. Abstract A26: Telomere length in normal and tumor breast tissue from BRCA2 mutation carriers and sporadic breast cancer cases Molecular Cancer Research. 14. DOI: 10.1158/1557-3125.Advbc15-A26 |
0.384 |
|
| 2013 |
Chen B, Gilbert LA, Cimini BA, Schnitzbauer J, Zhang W, Li GW, Park J, Blackburn EH, Weissman JS, Qi LS, Huang B. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell. 155: 1479-91. PMID 24360272 DOI: 10.1016/J.Cell.2013.12.001 |
0.536 |
|
| 2013 |
Belin BJ, Cimini BA, Blackburn EH, Mullins RD. Visualization of actin filaments and monomers in somatic cell nuclei. Molecular Biology of the Cell. 24: 982-94. PMID 23447706 DOI: 10.1091/Mbc.E12-09-0685 |
0.412 |
|
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