MMV_Im2Im: An Open Source Microscopy Machine Vision Toolbox for Image-to-Image Transformation

The deep learning research in computer vision has been growing extremely fast in the past decade, many of which have been translated into novel image analysis methods for biomedical problems. Broadly speaking, many deep learning based biomedical image analysis methods can be considered as a general image-to-image transformation framework. In this work, we introduce a new open source python package MMV_Im2Im for image-to-image transformation in bioimaging applications. The overall package is designed with a generic image-to-image transformation framework, which could be directly used for semantic segmentation, instance segmentation, image restoration, image generation, etc.. The implementation takes advantage of the state-of-the-art machine learning engineering techniques for users to focus on the research without worrying about the engineering details. We demonstrate the effectiveness of MMV_Im2Im in more than ten different biomedical problems. For biomedical machine learning researchers, we hope this new package could serve as the starting point for their specific problems to stimulate new biomedical image analysis or machine learning methods. For experimental biomedical researchers, we hope this work can provide a holistic view of the image-to-image transformation concept with diverse examples, so that deep learning based image-to-image transformation could be further integrated into the assay development process and permit new biomedical studies that can hardly be done only with traditional experimental methods. Source code can be found at https://github.com/MMV-Lab/mmv_im2im.