Journal Article

FZJ-2016-05127

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments

Sachs, C. C.FZJ* ; Grünberger, A.FZJ* ; Helfrich, S.FZJ* ; Probst, C.FZJ* ; Wiechert, W.FZJ* ; Kohlheyer, D. (Corresponding author)FZJ* ; Nöh, K. (Corresponding author)FZJ*

2016
PLoS Lawrence, Kan.

This record in other databases:      

Please use a persistent id in citations: http://hdl.handle.net/2128/12459  doi:10.1371/journal.pone.0163453

Abstract: BackgroundMicrofluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool.ResultsWe present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks.

---

Contributing Institute(s):

1. Biotechnologie (IBG-1)

Research Program(s):

1. 583 - Innovative Synergisms (POF3-583) (POF3-583)

Appears in the scientific report 2016

---

Database coverage:
; ; ; ; BIOSIS Previews ; DOAJ Seal ; Ebsco Academic Search ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection ; Zoological Record

---