Publications

Preprints
R Hollandi, A Szkalisity, T Toth, E Tasnadi, C Molnar, B Mathe, Grexa I, Molnar J, Balind A, Gorbe M, M Kovacs, Migh E, A Goodman, T Balassa, K Koos, W Wang, N Bara, F Kovacs, L Paavolainen, T Danka, A Kirston, AE Carpenter, and P. Horvath. Preprints. “A deep learning framework for nucleus segmentation using image style transfer”.
2019
E Shlevkov, H Basu, MA Bray, Z Sun, W Wei, K Apaydin, KW Karhohs, PF Chen, JLM Smith, O Wiskow, K Roet, X Huang, K Eggan, Carpenter AE, RJ Kleiman, and TL Schwarz. 2019. “A High-Content Screen Identifies TPP1 and Aurora B as Regulators of Axonal Mitochondrial Transport.” Cell Reports. 28(12), 3224–3237.e5. Publisher's Version
JC Caicedo, A Goodman, KW Karhohs, BA Cimini, J Ackerman, M Haghighi, C Heng, T Becker, M Doan, C McQuin, M Rohban, S Singh, and Carpenter AE. 2019. “Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl.” Nature Methods. Publisher's Version
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Rohban MH, Shafqat-Abbasi H, Singh S, and Carpenter AE. 2019. “Capturing single-cell heterogeneity via data fusion improves image-based profiling.” Nature Communications. 10, 2082.
MW Lafarge, JC Caicedo, Carpenter AE, JPW Pluim, S Singh, and M Veta. 2019. “Capturing Single-Cell Phenotypic Variation via Unsupervised Representation Learning.” In Proceedings of Machine Learning Research, 102: Pp. 315–325.
Kulikov V, Guo SM, Stone M, Goodman A, Carpenter AE, Bathe M, and Lempitsky V. 2019. “DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images.” PLoS Computational Biology 15(5): e1007012.
JC Caicedo, J Roth, A Goodman, T Becker, KW Karhohs, M Broisin, C Molnar, C McQuin, S Singh, F Theis, and Carpenter AE. 2019. “Evaluation of Deep Learning Strategies for Nucleus Segmentation in Fluorescence Images.” Cytometry, 95: 952-965.
Nassar M, Doan M, Filby A, Wolkenhauer O, Fogg DK, Piasecka J, Thornton CA, Carpenter AE, Summers HD, Rees P, and Hennig H. 2019. “Label‐Free Identification of White Blood Cells Using Machine Learning.” Cytometry.
Doan M and Carpenter AE. 2019. “Leveraging machine vision in cell-based diagnostics to do more with less.” Nature Materials 18, 414–418.
Rueden CT, Ackerman J, Arena ET, Eglinger J, Cimini BA, Goodman A, Carpenter AE, and Eliceiri KW. 2019. “Scientific Community Image Forum: A discussion forum for scientific image software.” PLoS Biology.
2018
Becker T, Caicedo JC, Singh S, Weckmann M, and Carpenter AE. 2018. “Combining morphological and migration profiles of in vitro time-lapse data.” In 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), Pp. 965–968.
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Goldsborough P, Pawlowski N, Caicedo JC, Singh S, and Carpenter AE. 2018. “CytoGAN: Generative Modeling of Cell Images”. Publisher's Version
Vasilevich AS, Mourcin F, Mentink A, Hulshof F, Beijer N, Zhao Y, Levers M, Papenburg B, Singh S, Carpenter AE, Stamatialis D, Blitterswijk van C, Tarte K, and Boer de J. 2018. “Designed Surface Topographies Control ICAM-1 Expression in Tonsil-Derived Human Stromal Cells.” Front Bioeng Biotechnol. 6:87. Publisher's Version
Doan M, Vorobjev I, Rees P, Filby A, Wolkenhauer O, Goldfeld AE, Lieberman J, Barteneva N, Carpenter AE, and Hennig H. 2018. “Diagnostic Potential of Imaging Flow Cytometry.” Trends Biotechnol 112:39-45. Publisher's Version
Simm J, Klambauer G, Arany A, Steijaert M, Wegner JK, Gustin E, Chupakhin V, Chong YT, Vialard J, Buijnsters P, Velter I, Vapirev A, Singh S, Carpenter AE, Wuyts R, Hochreiter S, Moreau, and Ceulemans H. 2018. “Repurposed High-Throughput Images Enable Biological Activity Prediction For Drug Discovery.” Cell Chem Biol. Publisher's Version
Caicedo JC, McQuin C, Goodman A, Singh S, and Carpenter AE. 2018. “Weakly supervised learning of single-cell feature embeddings.” In 2018 IEEE Conference on Computer Vision and Pattern Recognition (CVPR) bioRxiv, Pp. 293431. Publisher's Version
Yang SJ, Berndl M, Michael Ando D, Barch M, Narayanaswamy A, Christiansen E, Hoyer S, Roat C, Hung J, Rueden CT, Shankar A, Finkbeiner S, and Nelson P. 2018. “Assessing microscope image focus quality with deep learning.” BMC Bioinformatics 19(1):28962. Publisher's Version
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, and Carpenter AE. 2018. “CellProfiler 3.0: Next-generation image processing for biology.” PLoS Biol. 16(7):e2005970. Publisher's Version
Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P-M, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, and Greene CS. 2018. “Opportunities and obstacles for deep learning in biology and medicine.” J R Soc Interface 15(141). Publisher's Version

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