Bridging the Gap: Integrating Cutting-edge Techniques into Biological Imaging with deepImageJ
Authors: Fuster-Barceló Caterina , García López de Haro Carlos , Gómez-de-Mariscal Estibaliz , Ouyang Wei , Olivo-Marin Jean-Christophe , Sage Daniel , Muñoz-Barrutia Arrate 
Published: January 2024

AbstractThis manuscript showcases the latest advancements in deepImageJ, a pivotal Fiji/ImageJ plugin for bioimage analysis in the life sciences. The plugin, known for its user-friendly interface, facilitates the application of diverse pre-trained neural networks to custom data. The manuscript demonstrates a number of deepImageJ capabilities, particularly in executing complex pipelines, 3D analysis, and processing large images.A key development is the integration of the Java Deep Learning Library (JDLL), expanding deepImageJ’s compatibility with various deep learning frameworks, including TensorFlow, PyTorch, and ONNX. This allows for running multiple engines within a single Fiji/ImageJ instance, streamlining complex bioimage analysis tasks.The manuscript details three case studies to demonstrate these capabilities. The first explores integrated image-to image translation and nuclei segmentation. The second focuses on 3D nuclei segmentation. The third case study deals with large image segmentation.These studies underscore deepImageJ’s versatility and power in bioimage analysis, emphasizing its role as a critical tool for life scientists and researchers. The advancements in deepImageJ bridge the gap between deep learning model developers and end-users, enabling a more accessible and efficient approach to biological image analysis.The advancements in deepImageJ, detailed in this paper, represent a significant leap in bioimage analysis, crucial for life sciences. By enhancing this Fiji/ImageJ plugin, the research bridges the gap between complex deep learning models and practical applications, making advanced bioimage analysis accessible to a broader audience. This integration of the Java Deep Learning Library (JDLL) within deepImageJ is particularly noteworthy, as it expands compatibility with leading deep learning frameworks. This allows for the seamless execution of multiple models in a single instance, simplifying the construction of complex image analysis pipelines. The implications of this research are far-reaching, extending beyond academic circles to potentially impact various sectors, including healthcare, pharmaceuticals, and biotechnology. The enhanced capabilities of deepImageJ in handling intricate pipelines, 3D analysis, and large images facilitate detailed and efficient analysis of biological data. Such advancements are vital for accelerating research and development in medical imaging, drug discovery, and understanding complex biological processes. This manuscript contribution to the field of bioimage analysis is significant, offering a tool that empowers researchers, irrespective of their computational expertise, to leverage advanced technologies in their work. The wide applicability and ease of use of deepImageJ have the potential to foster interdisciplinary collaborations, drive innovation, and facilitate discoveries across various scientific and industrial sectors.