CellSium: versatile cell simulator for microcolony ground truth generation

Bioinformatics Advances, vol. 2, pp. vbac053

Abstract

Abstract Summary To train deep learning-based segmentation models, large ground truth datasets are needed. To address this need in microfluidic live-cell imaging, we present CellSium, a flexibly configurable cell simulator built to synthesize realistic image sequences of bacterial microcolonies growing in monolayers. We illustrate that the simulated images are suitable for training neural networks. Synthetic time-lapse videos with and without fluorescence, using programmable cell growth models, and simulation-ready 3D colony geometries for computational fluid dynamics are also supported. Availability and implementation CellSium is free and open source software under the BSD license, implemented in Python, available at github.com/modsim/cellsium (DOI: 10.5281/zenodo.6193033), along with documentation, usage examples and Docker images. Supplementary information Supplementary data are available at Bioinformatics Advances online.

Authors 6

1. Christian Carsten Sachs

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany

2. Karina Ruzaeva Aachen Aachen Institute for Advanced Study in Computational Engineering Science (AICES)

   Forschungszentrum Jülich · Aachen Institute for Advanced Study in Computational Engineering Science · RWTH Aachen University

   Affiliation as printed

   Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University , 52062 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany

   Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany

3. Johannes Seiffarth Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52074 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany

4. Wolfgang Wiechert Aachen Computational Systems Biotechnology

   Forschungszentrum Jülich · RWTH Aachen University

   Affiliation as printed

   Computational Systems Biotechnology (AVT.CSB), RWTH Aachen University , 52074 Aachen, Germany

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany

5. Benjamin Berkels Aachen Aachen Institute for Advanced Study in Computational Engineering Science (AICES)

   Aachen Institute for Advanced Study in Computational Engineering Science · RWTH Aachen University

   Affiliation as printed

   Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University , 52062 Aachen, Germany

6. Katharina Nöh corresponding

   Forschungszentrum Jülich

   Affiliation as printed

   Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH , 52425 Jülich, Germany