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@ARTICLE{Sachs:909145,
      author       = {Sachs, Christian Carsten and Ruzaeva, Karina and Seiffarth,
                      Johannes and Wiechert, Wolfgang and Berkels, Benjamin and
                      Nöh, Katharina},
      title        = {{C}ell{S}ium – versatile cell simulator for microcolony
                      ground truth generation},
      journal      = {Bioinformatics advances},
      volume       = {2},
      number       = {1},
      issn         = {2635-0041},
      address      = {Oxford},
      publisher    = {Oxford University Press},
      reportid     = {FZJ-2022-03031},
      pages        = {vbac053},
      year         = {2022},
      note         = {Funding: - Deutsche Forschungsgemeinschaft [WI 1705/16-2],
                      [491111487]- the President’s Initiative and Networking
                      Funds of the Helmholtz Association of German Research
                      Centres [SATOMI ZT-I-PF-04-011]- Helmholtz School for Data
                      Science in Life, Earth and Energy (HDS-LEE)},
      abstract     = {To train deep learning based segmentation models, large
                      ground truth data sets 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 (CFD) are also
                      supported.},
      cin          = {IBG-1},
      ddc          = {004},
      cid          = {I:(DE-Juel1)IBG-1-20101118},
      pnm          = {2172 - Utilization of renewable carbon and energy sources
                      and engineering of ecosystem functions (POF4-217)},
      pid          = {G:(DE-HGF)POF4-2172},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {36699390},
      UT           = {WOS:001153137500029},
      doi          = {10.1093/bioadv/vbac053},
      url          = {https://juser.fz-juelich.de/record/909145},
}