Software

Computer vision and machine learning software

  • CellCognition

    CellCognition is an open source software that combines object detection, classification of morphologies, and single-cell tracking. This enables measurements of progression through morphology stages and kinetic readouts at the single-cell level. The software was designed to run on three major platforms (Windows, Mac OS X, Linux) at high speed with high convenience. We therefore combined C++ image processing based on VIGRA with a Python-based workflow engine and a Qt-based graphical user-interface. To enable interoperability between different software platforms, we developed the standardized data exchange format CellH5, which stores high-dimensional image data along with inter-object relations in graphs. Please reference the CellCognition software by the original publication Held et al., Nature Methods, 2010.

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    Figure 1 (click to view legend)

References

CellCognition: time-resolved phenotype annotation in high-throughput live cell imaging. (2010). Held M, Schmitz MH, Fischer B, Walter T, Neumann B, Olma MH, Peter M, Ellenberg J, Gerlich DW. Nat Methods. 7(9):747-54

Unsupervised modeling of cell morphology dynamics for time-lapse microscopy. (2012). Zhong Q, Busetto AG, Fededa JP, Buhmann JM, Gerlich DW. Nat Methods. 9(7):711-3

CellH5: a format for data exchange in high-content screening. (2013). Sommer C, Held M, Fischer B, Huber W, Gerlich DW. Bioinformatics. 29(12):1580-2

Automated microscopy for high-content RNAi screening. (2010). Conrad C, Gerlich DW. J Cell Biol. 188(4):453-61.

Machine learning in cell biology - teaching computers to recognize phenotypes. (2013). Sommer C, Gerlich DW. J Cell Sci. 126(Pt 24):5529-39

 

Application examples

Cuylen, S., Blaukopf, C., Politi, AZ., Müller-Reichert, T., Neumann, B., Poser, I., Ellenberg, J., Hyman, AA., Gerlich, DW. (2016). Ki-67 acts as a biological surfactant to disperse mitotic chromosomes. Nature. [Epub ahead of print]

Sds22 and Repo-Man stabilize chromosome segregation by counteracting Aurora B on anaphase kinetochores. (2012). Wurzenberger C, Held M, Lampson MA, Poser I, Hyman AA, Gerlich DW. J Cell Biol. 198(2):173-83

RNAi-based screening identifies the Mms22L-Nfkbil2 complex as a novel regulator of DNA replication in human cells. (2010). Piwko W, Olma MH, Held M, Bianco JN, Pedrioli PG, Hofmann K, Pasero P, Gerlich DW, Peter M. EMBO J. 29(24):4210-22.

Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells. (2010). Schmitz MH, Held M, Janssens V, Hutchins JR, Hudecz O, Ivanova E, Goris J, Trinkle-Mulcahy L, Lamond AI, Poser I, Hyman AA, Mechtler K, Peters JM, Gerlich DW. Nat Cell Biol. 12(9):886-93.

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