SoftwareXBioinformaticsPeer-reviewed journal article
ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud
Johannes SeiffarthiD, Tim ScherriD, Bastian WollenhauptiD, Oliver NeumanniD, Hanno ScharriD, Dietrich KohlheyeriD, Ralf MikutiD, Katharina NöhiD
Abstract
SummaryReliable deep learning segmentation for microfluidic live-cell imaging requires comprehensive ground truth data. ObiWan-Microbi is a microservice platform combining the strength of state-of-the-art technologies into a unique integrated workflow for data management and efficient ground truth generation for instance segmentation, empowering collaborative semi-automated image annotation in the cloud. Availability and ImplementationObiWan-Microbi is open-source and available under the MIT license at https://github.com/hip-satomi/ObiWan-Microbi, along documentation and usage examples. Contactk.noeh@fz-juelich.de Supplementary informationSupplementary data are available online.
- assay: imaging
- research focus: cell-cell communication
- research focus: benchmarking
- research focus: software / tool
- approach: deep learning
- approach: experimental assay
- Citations
- 11
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