PartSeg v2: Bioimage Segmentation Using Advanced Deep Learning Techniques

In this paper, we present a new version of our bioimaging tool PartSeg. It allows integration of deep learning models from the Bioimage Model Zoo, which is a community-driven AI model repository. We also show how PartSeg’s power users can train such models, for example, to increase automatization of their data processing workflows. Then, we present further new features of PartSeg that make it easier to publish datasets in a durable and referencable way with version tracking. We also describe good practices related to data publishing and how adding metadata can allow for easier data discovery. Availability of such published datasets enables development of even better machine learning models. Publishing of the data is also a requirement for verifiable and repeatable science, leads to greater visibility of the results and enables cooperation and cross-domain exchange of ideas.