BIOMEDICAL IMAGING GROUP (BIG)
Laboratoire d'imagerie biomédicale (LIB)

DeepImageJ: A User-Friendly Plugin to Run Deep Learning Models in ImageJ

E. Gómez-de-Mariscal, C. García-López-de-Haro, L. Donati, M. Unser, A. Muñoz-Barrutia, D. Sage

Spanish & Portuguese Advanced Optical Microscopy Meeting 2020 (SPAOM'20), Valencia, Kingdom of Spain, Virtual, November 24-27, 2020.

The use of Deep Learning models requires previous programming knowledge and expertise, which makes them unapproachable to the general public. We present DeepImageJ, an open-source project that enables the generic use of pre-trained deep learning models provided by their developers in FIJI/ImageJ. The plugin acts as a software layer between TensorFlow and FIJI/ImageJ with all the technicalities hidden behind a user-friendly interface. In this workshop we show the two main functionalities of DeepImageJ: (1) a model importer tool that gathers all critical information from developers to get a correct image processing, and (2) a user-oriented tool that runs a selected model on an image batch. The plugin can also be called in a standard ImageJ/Fiji macro, which permits its inclusion as a standard plugin in image analysis workflows. This design facilitates the use of DNN models by end-users. 

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AUTHOR="G{\'{o}}mez-de-Mariscal, E. and
	Garc{\'{i}}a-L{\'{o}}pez-de-Haro, C. and Donati, L. and Unser, M.
	and Mu{\~{n}}oz-Barrutia, A. and Sage, D.",
TITLE="{DeepImageJ}: {A} User-Friendly Plugin to Run Deep Learning
	Models in {ImageJ}",
BOOKTITLE="Spanish \& Portuguese Advanced Optical Microscopy Meeting
	2020 ({SPAOM'20})",
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address="Valencia, Kingdom of Spain",
month="November 24-27,",
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