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bioRxiv · 10.1101/799270

DeepImageJ: A user-friendly plugin to run deep learning models in ImageJ

Gomez de Mariscal, E.·Garcia-Lopez-de-Haro, C.·Donati, L.·Unser, M.·Munoz-Barrutia, A.·Sage, D.
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Abstract

DeepImageJ is a user-friendly solution that enables the generic use of pre-trained deep learn ing (DL) models for biomedical image analysis in ImageJ. The deepImageJ environment gives access to the largest bioimage repository of pre-trained DL models (BioImage Model Zoo). Hence, non-experts can easily perform common image processing tasks in life-science research with DL-based tools including pixel and object classification, instance segmentation, denoising or virtual staining. DeepImageJ is compatible with existing state-of-the-art solutions and it is equipped with utility tools for developers to include new models. Very recently, several train ing frameworks have adopted the deepImageJ format to deploy their work in one of the most used software in the field (ImageJ). Beyond its direct use, we expect deepImageJ to contribute to the broader dissemination and reuse of DL models in life-sciences applications and bioimage informatics.

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Gomez de Mariscal, E., Garcia-Lopez-de-Haro, C., Donati, L., Unser, M., Munoz-Barrutia, A., Sage, D.. 2019-10-16. DeepImageJ: A user-friendly plugin to run deep learning models in ImageJ. https://doi.org/10.1101/799270

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