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@ARTICLE{Jansen:890775,
      author       = {Jansen, Roman and Küsters, Kira and Morschett, Holger and
                      Wiechert, Wolfgang and Oldiges, Marco},
      title        = {{A} fully automated pipeline for the dynamic at-line
                      morphology analysis of microscale {A}spergillus cultivation},
      journal      = {Fungal Biology and Biotechnology},
      volume       = {8},
      number       = {2},
      issn         = {2054-3085},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {FZJ-2021-01191},
      pages        = {1-10},
      year         = {2021},
      abstract     = {BackgroundMorphology, being one of the key factors
                      influencing productivity of filamentous fungi, is of great
                      interest during bioprocess development. With increasing
                      demand of high-throughput phenotyping technologies for fungi
                      due to the emergence of novel time-efficient genetic
                      engineering technologies, workflows for automated liquid
                      handling combined with high-throughput morphology analysis
                      have to be developed.ResultsIn this study, a protocol
                      allowing for 48 parallel microbioreactor cultivations of
                      Aspergillus carbonarius with non-invasive online signals of
                      backscatter and dissolved oxygen was established. To handle
                      the increased cultivation throughput, the utilized
                      microbioreactor is integrated into a liquid handling
                      platform. During cultivation of filamentous fungi, cell
                      suspensions result in either viscous broths or form pellets
                      with varying size throughout the process. Therefore,
                      tailor-made liquid handling parameters such as
                      aspiration/dispense height, velocity and mixing steps were
                      optimized and validated. Development and utilization of a
                      novel injection station enabled a workflow, where biomass
                      samples are automatically transferred into a flow through
                      chamber fixed under a light microscope. In combination with
                      an automated image analysis concept, this enabled an
                      automated morphology analysis pipeline. The workflow was
                      tested in a first application study, where the projected
                      biomass area was determined at two different cultivation
                      temperatures and compared to the microbioreactor online
                      signals.ConclusionsA novel and robust workflow starting from
                      microbioreactor cultivation, automated sample harvest and
                      processing via liquid handling robots up to automated
                      morphology analysis was developed. This protocol enables the
                      determination of projected biomass areas for filamentous
                      fungi in an automated and high-throughput manner. This
                      measurement of morphology can be applied to describe overall
                      pellet size distribution and heterogeneity.},
      cin          = {IBG-1},
      ddc          = {630},
      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       = {33676585},
      doi          = {10.1186/s40694-021-00109-4},
      url          = {https://juser.fz-juelich.de/record/890775},
}