| Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system B Chen, LA Gilbert, BA Cimini, J Schnitzbauer, W Zhang, GW Li, J Park, ... Cell 155 (7), 1479-1491, 2013 | 2332 | 2013 |
| CellProfiler 3.0: Next-generation image processing for biology C McQuin, A Goodman, V Chernyshev, L Kamentsky, BA Cimini, ... PLoS biology 16 (7), e2005970, 2018 | 1956 | 2018 |
| CellProfiler 4: improvements in speed, utility and usability DR Stirling, MJ Swain-Bowden, AM Lucas, AE Carpenter, BA Cimini, ... BMC Bioinformatics 22 (1), 1-11, 2021 | 1257 | 2021 |
| Genetic and transcriptional evolution alters cancer cell line drug response U Ben-David, B Siranosian, G Ha, H Tang, Y Oren, K Hinohara, ... Nature 560 (7718), 325-330, 2018 | 894 | 2018 |
| Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl JC Caicedo, A Goodman, KW Karhohs, BA Cimini, J Ackerman, ... Nature methods 16 (12), 1247-1253, 2019 | 711 | 2019 |
| Metrics reloaded: recommendations for image analysis validation L Maier-Hein, A Reinke, P Godau, MD Tizabi, F Buettner, E Christodoulou, ... Nature methods, 1-18, 2024 | 298* | 2024 |
| Common limitations of image processing metrics: A picture story A Reinke, MD Tizabi, CH Sudre, M Eisenmann, T Rädsch, M Baumgartner, ... arXiv preprint arXiv:2104.05642, 2021 | 207 | 2021 |
| Visualization of actin filaments and monomers in somatic cell nuclei BJ Belin, BA Cimini, EH Blackburn, RD Mullins Molecular biology of the cell 24 (7), 982-994, 2013 | 175 | 2013 |
| CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis DR Stirling, AE Carpenter, BA Cimini Bioinformatics 37 (21), 3992-3994, 2021 | 114 | 2021 |
| Understanding metric-related pitfalls in image analysis validation A Reinke, MD Tizabi, M Baumgartner, M Eisenmann, D Heckmann-Nötzel, ... Nature methods 21 (2), 182-194, 2024 | 91 | 2024 |
| Morphology and gene expression profiling provide complementary information for mapping cell state GP Way, T Natoli, A Adeboye, L Litichevskiy, A Yang, X Lu, JC Caicedo, ... Cell Systems, 2022 | 88 | 2022 |
| Optimizing the Cell Painting assay for image-based profiling BA Cimini, SN Chandrasekaran, M Kost-Alimova, L Miller, A Goodale, ... Nature protocols 18 (7), 1981-2013, 2023 | 84 | 2023 |
| High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations M Haghighi, JC Caicedo, BA Cimini, AE Carpenter, S Singh Nature Methods, 1-8, 2022 | 77 | 2022 |
| Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin JS Wang, T Kamath, CM Mazur, F Mirzamohammadi, D Rotter, H Hojo, ... Nature Communications 12 (1), 1-20, 2021 | 74 | 2021 |
| Three million images and morphological profiles of cells treated with matched chemical and genetic perturbations SN Chandrasekaran, BA Cimini, A Goodale, L Miller, M Kost-Alimova, ... Nature Methods, 1-8, 2024 | 71 | 2024 |
| The multimodality cell segmentation challenge: toward universal solutions J Ma, R Xie, S Ayyadhury, C Ge, A Gupta, R Gupta, S Gu, Y Zhang, G Lee, ... Nature Methods, 1-11, 2024 | 71 | 2024 |
| Learning representations for image-based profiling of perturbations N Moshkov, M Bornholdt, S Benoit, M Smith, C McQuin, A Goodman, ... Nature Communications 15 (1), 1594, 2024 | 71 | 2024 |
| OME-Zarr: a cloud-optimized bioimaging file format with international community support J Moore, D Basurto-Lozada, S Besson, J Bogovic, J Bragantini, EM Brown, ... Histochemistry and Cell Biology 160 (3), 223-251, 2023 | 71 | 2023 |
| Open-source deep-learning software for bioimage segmentation AM Lucas, PV Ryder, B Li, BA Cimini, KW Eliceiri, AE Carpenter Molecular Biology of the Cell 32 (9), 823-829, 2021 | 69 | 2021 |
| JUMP Cell Painting dataset: morphological impact of 136,000 chemical and genetic perturbations SN Chandrasekaran, J Ackerman, E Alix, DM Ando, J Arevalo, M Bennion, ... bioRxiv, 2023.03. 23.534023, 2023 | 65 | 2023 |
Anne E. CarpenterInstitute Scientist and Imaging Platform Director, Broad Institute of Harvard and MITVerified email at broadinstitute.org