DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible

Hidalgo-Cenalmor, I.; Pylvänäinen, J. W.; Ferreira, M. G.; Russell, C. T.; Arganda-Carreras, I.; AI4Life Consortium,; Jacquemet, G.; Henriques, R.; Gomez-de-Mariscal, E.

doi:10.1101/2023.11.19.567606

bioRxiv · 10.1101/2023.11.19.567606

DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible

Hidalgo-Cenalmor, I.·Pylvänäinen, J. W.·Ferreira, M. G.·Russell, C. T.·Arganda-Carreras, I.·AI4Life Consortium,·Jacquemet, G.·Henriques, R.·Gomez-de-Mariscal, E.

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Abstract

Deep learning has revolutionised the analysis of extensive microscopy datasets, yet challenges persist in the widespread adoption of these techniques. Many lack access to training data, computing resources, and expertise to develop complex models. We introduce DL4MicEverywhere, advancing our previous ZeroCostDL4Mic platform, to make deep learning more accessible. DL4MicEverywhere uniquely allows flexible training and deployment across diverse computational environments by encapsulating methods in interactive Jupyter notebooks within Docker containers -a standalone virtualisation of required packages and code to reproduce a computational environment-. This enhances reproducibility and convenience. The platform includes twice as many techniques as originally provided by ZeroCostDL4Mic and enables community contributions via automated build pipelines. DL4MicEverywhere empowers participatory innovation and aims to democratise deep learning for bioimage analysis.

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Hidalgo-Cenalmor, I., Pylvänäinen, J. W., Ferreira, M. G., Russell, C. T., Arganda-Carreras, I., AI4Life Consortium,, Jacquemet, G., Henriques, R., Gomez-de-Mariscal, E.. 2023-11-19. DL4MicEverywhere: Deep learning for microscopy made flexible, shareable, and reproducible. https://doi.org/10.1101/2023.11.19.567606

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