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Imaging Platform

An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells.

Dordea AC, Bray MA, Allen K, et al. An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells. Exp Eye Res. 2016;147:50-6. doi:10.1016/j.exer.2016.04.012

Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification.

Logan DJ, Shan J, Bhatia SN, Carpenter AE. Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Methods. 2016;96:6-11. doi:10.1016/j.ymeth.2015.12.002

CP-CHARM: segmentation-free image classification made accessible.

Uhlmann V, Singh S, Carpenter AE. CP-CHARM: segmentation-free image classification made accessible. BMC Bioinformatics. 2016;17:51. doi:10.1186/s12859-016-0895-y

A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells.

Jolly AL, Luan CH, Dusel BE, et al. A Genome-wide RNAi Screen for Microtubule Bundle Formation and Lysosome Motility Regulation in Drosophila S2 Cells. Cell Rep. 2016;14(3):611-20. doi:10.1016/j.celrep.2015.12.051

Label-free cell cycle analysis for high-throughput imaging flow cytometry.

Blasi T, Hennig H, Summers HD, et al. Label-free cell cycle analysis for high-throughput imaging flow cytometry. Nat Commun. 2016;7:10256. doi:10.1038/ncomms10256

Automating Morphological Profiling with Generic Deep Convolutional Networks.

Pawlowski N, Caicedo J, Singh S, Carpenter A, Storkey A. Automating Morphological Profiling with Generic Deep Convolutional Networks. bioRxiV. 2016. doi:10.1101/085118

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.

Bray MA, Carpenter AE. CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data. BMC Bioinformatics. 2015;16:368. doi:10.1186/s12859-015-0759-x

CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells.

Jeong YM, Duanting Z, Hennig H, et al. CDy6, a photostable probe for long-term real-time visualization of mitosis and proliferating cells. Chem Biol. 2015;22(2):299-307. doi:10.1016/j.chembiol.2014.11.018

Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images.

Bray MA, Vokes MS, Carpenter AE. Using CellProfiler for Automatic Identification and Measurement of Biological Objects in Images. Curr Protoc Mol Biol. 2015;109:14.17.1-13. doi:10.1002/0471142727.mb1417s109

Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects.

Singh S, Wu X, Ljosa V, et al. Morphological Profiles of RNAi-Induced Gene Knockdown Are Highly Reproducible but Dominated by Seed Effects. PLoS One. 2015;10(7):e0131370. doi:10.1371/journal.pone.0131370