ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud (ObiWan-Microbi)
Authors: Johannes Seiffarth, Tim Scherr, Bastian Wollenhaupt, Oliver Neumann, Hanno Scharr, Dietrich Kohlheyer, Ralf Mikut, Katharina Nöh
ObiWan-Microbi: OMERO-based integrated Workflow for annotating Microbes in the Cloud
ObiWan-Microbi is a toolkit collection for semi-automated segmentation and annotation of (biological) time-lapse image data in the cloud. It utilizes an OMERO image server for data management. We contribute SegUI - a browser-based tool for semi-automated manual segmentation and annotation - and SegServe - a remote neural network execution server. All three components are combined into a docker-compose setup to be easily deployed on a local computer or in a cloud system.
Publications
ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud
Seiffarth J, Scherr T, Wollenhaupt B, Neumann O, Scharr H, Kohlheyer D, Mikut R, Nöh K - SoftwareX - 2024
License
MIT
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