ObiWan-Microbi: OMERO-based integrated workflow for annotating microbes in the cloud

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Summary Reliable 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 Implementation ObiWan-Microbi is open-source and available under the MIT license at https://github.com/hip-satomi/ObiWan-Microbi , along documentation and usage examples. Contact k.noeh@fz-juelich.de Supplementary information Supplementary data are available online.

Authors 8

1. Johannes Seiffarth Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University, Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

   Institute of Bio- and Geosciences, IBG-: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

2. Tim Scherr

   Karlsruhe Institute of Technology

   Affiliation as printed

   Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany

3. Bastian Wollenhaupt

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

   Institute of Bio- and Geosciences, IBG-: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

4. Oliver Neumann

   Karlsruhe Institute of Technology

   Affiliation as printed

   Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany

5. Hanno Scharr

   Forschungszentrum Jülich

   Affiliation as printed

   Institute for Advanced Simulation, IAS-8, Forschungszentrum Jülich GmbH, Jülich, Germany

6. Dietrich Kohlheyer Aachen Microscale Bioengineering (AVT-MSB)

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

   Microscale Bioengineering (AVT-MSB), RWTH Aachen University, Aachen, German

   Institute of Bio- and Geosciences, IBG-: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

7. Ralf Mikut

   Karlsruhe Institute of Technology

   Affiliation as printed

   Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany

8. Katharina Nöh corresponding

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany

   Institute of Bio- and Geosciences, IBG-: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany