Computational protocol: Structure–function analysis of the extracellular domain of the pneumococcal cell division site positioning protein MapZ

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Protocol publication

[…] Microscopy was performed on exponentially growing cells (OD550=0.15). Slides were visualized using a Zeiss AxioObserver Z1 microscope fitted with an Orca-R2 C10600 charge-coupled device (CCD) camera (Hamamatsu), with a × 100 numerical aperture 1.46 objective. Images were collected using Axiovision (Carl Zeiss), convolved using ImageJ (http://rsb.info.nih.gov/ij/) and analysed using Coli-Inspector (detection was approved manually) running under the plugin ObjectJ (http://simon.bio.uva.nl/objectj/) to generate fluorescent intensity linescans sorted with respect to cell length. The MicrobeTracker suite extended by custom MATLAB routines was used to generate cell width/length ratio. Selected images are representative of experiments made in triplicate. […]

Pipeline specifications

Software tools ImageJ, ObjectJ, MicrobeTracker
Application Microscopic phenotype analysis
Organisms Bacteria, Streptococcus pneumoniae
Chemicals Amino Acids