| CellProfiler 3.0: Next-generation image processing for biology C McQuin, A Goodman, V Chernyshev, L Kamentsky, BA Cimini, ... PLoS biology 16 (7), 2018 | 1861 | 2018 |
| Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes MA Bray, S Singh, H Han, CT Davis, B Borgeson, C Hartland, ... Nature Protocols 11 (9), 1757-1774, 2016 | 821 | 2016 |
| Data-analysis strategies for image-based cell profiling JC Caicedo, S Cooper, F Heigwer, S Warchal, P Qiu, C Molnar, ... Nature methods 14 (9), 849-863, 2017 | 669 | 2017 |
| 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 | 641 | 2019 |
| Evaluation of deep learning strategies for nucleus segmentation in fluorescence images JC Caicedo, J Roth, A Goodman, T Becker, KW Karhohs, M Broisin, ... Cytometry Part A 95 (9), 952-965, 2019 | 310 | 2019 |
| Increasing the Content of High-Content Screening An Overview S Singh, AE Carpenter, A Genovesio Journal of biomolecular screening 19 (5), 640-650, 2014 | 246 | 2014 |
| Repurposing high-throughput image assays enables biological activity prediction for drug discovery J Simm, G Klambauer, A Arany, M Steijaert, JK Wegner, E Gustin, ... Cell chemical biology 25 (5), 611-618. e3, 2018 | 231 | 2018 |
| High-throughput phenotyping of lung cancer somatic mutations AH Berger, AN Brooks, X Wu, Y Shrestha, C Chouinard, F Piccioni, ... Cancer Cell 30 (2), 214-228, 2016 | 225 | 2016 |
| Comparison of methods for image-based profiling of cellular morphological responses to small-molecule treatment V Ljosa, PD Caie, R ter Horst, KL Sokolnicki, EL Jenkins, S Daya, ... Journal of biomolecular screening 18 (10), 1321-1329, 2013 | 191 | 2013 |
| Canonical and atypical E2Fs regulate the mammalian endocycle HZ Chen, MM Ouseph, J Li, T Pécot, V Chokshi, L Kent, S Bae, M Byrne, ... Nature Cell Biology, 2012 | 177 | 2012 |
| Applications in image-based profiling of perturbations JC Caicedo, S Singh, AE Carpenter Current Opinion in Biotechnology 39, 134-142, 2016 | 173 | 2016 |
| A dataset of images and morphological profiles of 30 000 small-molecule treatments using the Cell Painting assay MA Bray, SM Gustafsdottir, MH Rohban, S Singh, V Ljosa, KL Sokolnicki, ... GigaScience 6 (12), giw014, 2017 | 159 | 2017 |
| CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets D Dao, AN Fraser, J Hung, V Ljosa, S Singh, AE Carpenter Bioinformatics 32 (20), 3210-3212, 2016 | 144 | 2016 |
| Systematic morphological profiling of human gene and allele function via Cell Painting MH Rohban, S Singh, X Wu, JB Berthet, MA Bray, Y Shrestha, X Varelas, ... eLife 6, e24060, 2017 | 139 | 2017 |
| Pipeline for illumination correction of images for high‐throughput microscopy S Singh, MA Bray, TR Jones, AE Carpenter Journal of microscopy, 2014 | 124 | 2014 |
| Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence AK Barczak, R Avraham, S Singh, SS Luo, WR Zhang, MA Bray, ... PLoS Pathogens 13 (5), e1006363, 2017 | 108 | 2017 |
| Predicting cell health phenotypes using image-based morphology profiling GP Way, M Kost-Alimova, T Shibue, WF Harrington, S Gill, F Piccioni, ... Molecular Biology of the Cell 32 (9), 995-1005, 2021 | 102 | 2021 |
| Automating Morphological Profiling with Generic Deep Convolutional Networks N Pawlowski, JC Caicedo, S Singh, AE Carpenter, A Storkey bioRxiv, 085118, 2016 | 87 | 2016 |
| Weakly supervised learning of single-cell feature embeddings JC Caicedo, C McQuin, A Goodman, S Singh, AE Carpenter Proceedings of the IEEE Conference on Computer Vision and Pattern …, 2018 | 84 | 2018 |
| Anomaly detection using negative selection based on the r-contiguous matching rule S Singh 1st International Conference on Artificial Immune Systems (ICARIS …, 2002 | 81 | 2002 |
Anne E. CarpenterInstitute Scientist and Imaging Platform Director, Broad Institute of Harvard and MITVerified email at broadinstitute.org
