EPFL | Biomedical Imaging Group

Bridging the Gap: Integrating Cutting-Edge Techniques into Biological Imaging with deepImageJ

C. Fuster-Barceló, C. García-López-de-Haro, E. Gómez-de-Mariscal, W. Ouyang, J.-C. Olivo-Marin, D. Sage, A. Muñoz-Barrutia

Biological Imaging, vol. 4, paper no. e14, 15 p., November 22, 2024.

This manuscript showcases the latest advancements in deepImageJ, a pivotal Fiji/ImageJ plugin for bioimage analysis in life sciences. The plugin, known for its user-friendly interface, facilitates the application of diverse pre-trained convolutional neural networks to custom data. The manuscript demonstrates several deepImageJ capabilities, particularly in deploying complex pipelines, three-dimensional (3D) image analysis, and processing large images. A key development is the integration of the Java Deep Learning Library, expanding deepImageJ's compatibility with various deep learning (DL) frameworks, including TensorFlow, PyTorch, and ONNX. This allows for running multiple engines within a single Fiji/ImageJ instance, streamlining complex bioimage analysis workflows. The manuscript details three case studies to demonstrate these capabilities. The first case study explores integrated image-to-image translation followed by nuclei segmentation. The second case study focuses on 3D nuclei segmentation. The third case study showcases large image volume segmentation and compatibility with the BioImage Model Zoo. These use cases underscore deepImageJ's versatility and power to make advanced DLmore accessible and efficient for bioimage analysis. The new developments within deepImageJ seek to provide a more flexible and enriched user-friendly framework to enable next-generation image processing in life science.

@ARTICLE(http://bigwww.epfl.ch/publications/fusterbarcelo2401.html,
AUTHOR="Fuster-Barcel{\'{o}}, C. and Garc{\'{i}}a-L{\'{o}}pez-de-Haro,
	C. and G{\'{o}}mez-de-Mariscal, E. and Ouyang, W. and Olivo-Marin,
	J.-C. and Sage, D. and Mu{\~{n}}oz-Barrutia, A.",
TITLE="Bridging the Gap: {I}ntegrating Cutting-Edge Techniques into
	Biological Imaging with {deepImageJ}",
JOURNAL="Biological Imaging",
YEAR="2024",
volume="4",
number="",
pages="",
month="November 22,",
note="paper no.\ e14")

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