microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation (microbeSEG)
microbeSEG is a deep learning-based tool for instance segmentation of roundish objects in 2D and 2D+t data, e.g., microbes. The microbeSEG workflow covers training data creation (with pre-labeling) or import, model training, model evaluation, and the final segmentation of the data. OMERO is used for a comprehensive data management. For training data annotation, the jointly developed toolkit collection ObiWan-Microbi is used.
Publications
microbeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation
Scherr T, Seiffarth J, Wollenhaupt B, Neumann O, Schilling M, Kohlheyer D, Scharr H, Nöh K, Mikut R - PLOS ONE - 2022
Helmholtz Imaging Projects
2020: SATOMI - Tackling the segmentation and tracking challenges of growing colonies and microbial diversity
Other solutions related to MicrobeSEG: A deep learning software tool with OMERO data management for efficient and accurate cell segmentation in Helmholtz Imaging CONNECT:
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 …
