Anne E. Carpenter

44 papers A* 5Journal 28Unranked 11

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Cubic: CUDA-Accelerated 3D Bioimage Computing. ICCVW Alexandr A. Kalinin, Anne E. Carpenter, Shantanu Singh, Matthew J. O'Meara
2025	J	`jnl`	Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling. CoRR Alexandr A. Kalinin, Paula Llanos, Theresa Maria Sommer, Giovanni Sestini, Xinhai Hou, Jonathan Z. Sexton, Xiang Wan, Ivo D. Dinov, Brian D. Athey, Nicolas Rivron, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Matthew J. O'Meara
2025	A*	`conf`	Learning Molecular Representation in a Cell. ICLR Gang Liu, Srijit Seal, John Arevalo, Zhenwen Liang, Anne E. Carpenter, Meng Jiang, Shantanu Singh
2025	A*	`conf`	MorphoDiff: Cellular Morphology Painting with Diffusion Models. ICLR Zeinab Navidi, Jun Ma, Esteban Miglietta, Le Liu, Anne E. Carpenter, Beth A. Cimini, Benjamin Haibe-Kains, Bo Wang
2025	J	`jnl`	cp_measure: API-first feature extraction for image-based profiling workflows. CoRR Alán F. Muñoz, Tim Treis, Alexandr A. Kalinin, Shatavisha Dasgupta, Fabian J. Theis, Anne E. Carpenter, Shantanu Singh
2025	J	`jnl`	cubic: CUDA-accelerated 3D Bioimage Computing. CoRR Alexandr A. Kalinin, Anne E. Carpenter, Shantanu Singh, Matthew J. O'Meara
2024	J	`jnl`	Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning. PLoS Comput. Biol. Robert van Dijk, John Arevalo, Mehrtash Babadi, Anne E. Carpenter, Shantanu Singh
2024	J	`jnl`	Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank. J. Chem. Inf. Model. Srijit Seal, Ola Spjuth, Layla Hosseini-Gerami, Miguel García-Ortegón, Shantanu Singh, Andreas Bender, Anne E. Carpenter
2024	J	`jnl`	Learning Molecular Representation in a Cell. CoRR Gang Liu, Srijit Seal, John Arevalo, Zhenwen Liang, Anne E. Carpenter, Meng Jiang, Shantanu Singh
2024	J	`jnl`	MOTI CoRR John Arevalo, Ellen Su, Anne E. Carpenter, Shantanu Singh
2024	A*	`conf`	MOTIVE: A Drug-Target Interaction Graph For Inductive Link Prediction. NeurIPS John Arevalo, Ellen Su, Anne E. Carpenter, Shantanu Singh
2023	A*	`conf`	Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. IJCAI Marzieh Haghighi, Mario C. Cruz, Erin Weisbart, Beth A. Cimini, Avtar Singh, Julia Bauman, Maria E. Lozada, Sanam L. Kavari, James T. Neal, Paul C. Blainey, Anne E. Carpenter, Shantanu Singh
2023	J	`jnl`	Pseudo-Labeling Enhanced by Privileged Information and Its Application to In Situ Sequencing Images. CoRR Marzieh Haghighi, Mario C. Cruz, Erin Weisbart, Beth A. Cimini, Avtar Singh, Julia Bauman, Maria E. Lozada, Sanam L. Kavari, James T. Neal, Paul C. Blainey, Anne E. Carpenter, Shantanu Singh
2022	J	`jnl`	Predicting drug polypharmacology from cell morphology readouts using variational autoencoder latent space arithmetic. PLoS Comput. Biol. Yuen Ler Chow, Shantanu Singh, Anne E. Carpenter, Gregory P. Way
2021	J	`jnl`	A field guide to cultivating computational biology. CoRR Anne E. Carpenter, Casey S. Greene, Piero Carnici, Benilton S. Carvalho, Michiel de Hoon, Stacey D. Finley, Kim-Anh Lê Cao, Jerry S. H. Lee, Luigi Marchionni, Suzanne Sindi, Fabian J. Theis, Gregory P. Way, Jean Y. H. Yang, Elana J. Fertig
2021	J	`jnl`	CellProfiler 4: improvements in speed, utility and usability. BMC Bioinform. David R. Stirling, Madison J. Swain-Bowden, Alice M. Lucas, Anne E. Carpenter, Beth A. Cimini, Allen Goodman
2021	J	`jnl`	CellProfiler Analyst 3.0: accessible data exploration and machine learning for image analysis. Bioinform. David R. Stirling, Anne E. Carpenter, Beth A. Cimini
2021	J	`jnl`	Developing open-source software for bioimage analysis: opportunities and challenges. F1000Research Florian Levet, Anne E. Carpenter, Kevin W. Eliceiri, Anna Kreshuk, Peter Bankhead, Robert Haase
2020	J	`jnl`	Bridging Domain and Data. Patterns Anne E. Carpenter
2020	J	`jnl`	Keras R-CNN: library for cell detection in biological images using deep neural networks. BMC Bioinform. Jane Hung, Allen Goodman, Deepali Ravel, Stefanie Lopes, Gabriel Rangel, Odailton A. Nery, Benoit Malleret, Francois Nosten, Marcus V. G. Lacerda, Marcelo U. Ferreira, Laurent Rénia, Manoj Duraisingh, Fabio T. M. Costa, Matthias Marti, Anne E. Carpenter
2019	—	`conf`	Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning. MIDL Maxime W. Lafarge, Juan C. Caicedo, Anne E. Carpenter, Josien P. W. Pluim, Shantanu Singh, Mitko Veta
2019	J	`jnl`	DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. PLoS Comput. Biol. Victor Kulikov, Syuan-Ming Guo, Matthew Stone, Allen Goodman, Anne E. Carpenter, Mark Bathe, Victor S. Lempitsky
2018	J	`jnl`	Applying Faster R-CNN for Object Detection on Malaria Images. CoRR Jane Hung, Allen Goodman, Stefanie Lopes, Gabriel Rangel, Deepali Ravel, Fabio T. M. Costa, Manoj Duraisingh, Matthias Marti, Anne E. Carpenter
2018	—	`conf`	Combining morphological and migration profiles of in vitro time-lapse data. ISBI Tim Becker, Juan C. Caicedo, Shantanu Singh, Markus Weckmann, Anne E. Carpenter
2018	A*	`conf`	Weakly Supervised Learning of Single-Cell Feature Embeddings. CVPR Juan C. Caicedo, Claire McQuin, Allen Goodman, Shantanu Singh, Anne E. Carpenter
2017	—	`conf`	Applying Faster R-CNN for Object Detection on Malaria Images. CVPR Workshops Jane Hung, Anne E. Carpenter
2016	J	`jnl`	CP-CHARM: segmentation-free image classification made accessible. BMC Bioinform. Virginie Uhlmann, Shantanu Singh, Anne E. Carpenter
2016	J	`jnl`	CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. Bioinform. David Dao, Adam Fraser, Jane Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter
2016	J	`jnl`	QSAR-Driven Discovery of Novel Chemical Scaffolds Active against J. Chem. Inf. Model. Cleber C. Melo-Filho, Rafael Ferreira Dantas, Rodolpho C. Braga, Bruno Junior Neves, Mario R. Senger, Walter C. G. Valente, João M. Rezende-Neto, Willian T. Chaves, Eugene N. Muratov, Ross A. Paveley, Nicholas Furnham, Lee Kamentsky, Anne E. Carpenter, Floriano Silva-Junior, Carolina Horta Andrade
2015	—	`conf`	Analysis of High-throughput Microscopy Videos: Catching Up with Cell Dynamics. MICCAI (3) Assaf Arbelle, N. Drayman, Mark-Anthony Bray, Uri Alon, Anne E. Carpenter, Tammy Riklin Raviv
2015	J	`jnl`	CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. BMC Bioinform. Mark-Anthony Bray, Anne E. Carpenter
2015	—	`conf`	Symmetry-based mitosis detection in time-lapse microscopy. ISBI Topaz Gilad, Mark-Anthony Bray, Anne E. Carpenter, Tammy Riklin Raviv
2014	—	`conf`	Behavior in the Time of Cholera: Evidence from the 2008-2009 Cholera Outbreak in Zimbabwe. SBP Anne E. Carpenter
2014	J	`jnl`	ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments. Bioinform. Imtiaz A. Khan, Adam Fraser, Mark-Anthony Bray, Paul J. Smith, Nick S. White, Anne E. Carpenter, Rachel J. Errington
2011	—	`conf`	Extracting biomedically important information from large, automated imaging experiments. ISBI Anne E. Carpenter
2011	J	`jnl`	Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinform. Lee Kamentsky, Thouis R. Jones, Adam Fraser, Mark-Anthony Bray, David J. Logan, Katherine L. Madden, Vebjorn Ljosa, Curtis Rueden, Kevin W. Eliceiri, Anne E. Carpenter
2011	J	`jnl`	Visualization of Parameter Space for Image Analysis. IEEE Trans. Vis. Comput. Graph. A. Johannes Pretorius, Mark-Anthony Bray, Anne E. Carpenter, Roy A. Ruddle
2010	—	`conf`	Morphology-Guided Graph Search for Untangling Objects: MICCAI (3) Tammy Riklin Raviv, Vebjorn Ljosa, Annie L. Conery, Frederick M. Ausubel, Anne E. Carpenter, Polina Golland, Carolina Wählby
2010	—	`conf`	Resolving clustered worms via probabilistic shape models. ISBI Carolina Wählby, Tammy Riklin-Raviv, Vebjorn Ljosa, Annie L. Conery, Polina Golland, Frederick M. Ausubel, Anne E. Carpenter
2010	J	`jnl`	Towards automated high-throughput screening of C. elegans on agar CoRR Mayank Kabra, Annie L. Conery, Eyleen J. O'Rourke, Xin Xie, Vebjorn Ljosa, Thouis R. Jones, Frederick M. Ausubel, Gary Ruvkun, Anne E. Carpenter, Yoav Freund
2009	J	`jnl`	Introduction to the Quantitative Analysis of Two-Dimensional Fluorescence Microscopy Images for Cell-Based Screening. PLoS Comput. Biol. Vebjorn Ljosa, Anne E. Carpenter
2009	J	`jnl`	Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. Bioinform. Björn Nilsson, Mikael Johansson, Fátima Al-Shahrour, Anne E. Carpenter, Benjamin L. Ebert
2008	J	`jnl`	CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinform. Thouis R. Jones, In Han Kang, Douglas B. Wheeler, Robert A. Lindquist, Adam Papallo, David M. Sabatini, Polina Golland, Anne E. Carpenter
2005	—	`conf`	Voronoi-Based Segmentation of Cells on Image Manifolds. CVBIA Thouis R. Jones, Anne E. Carpenter, Polina Golland