Software

July12

Result of analyzing fixed DIC images of bacteria

Growth rate and cell size distributions. (a) The growth (log10 cell density) of E. coli MG1655 cells was measured as a function of time in the following growth media: LB (black), yeast extract broth (YEB) (red), tryptone broth (TB) (green), M9 media supplemented either with glucose (blue), succinate (brown) or acetate (purple). Samples taken from the mid-log phase (circles) (b) (left) were examined in DIC microscopy (scale bar, 5 µm) and (right) the cell length distribution (bars) plotted. The distribution was fit to lognormal (red) where μ: mean cell length, v, variance; n, total number of cells. dmax is the Kolmogorov–Smirnov test value evaluated for the fit.

Rod-shaped bacterial cell length analysis in MATLAB- automated routine. Needs parameter optimization. Image-mode: differential interference contrast (DIC). [github-code] [Ref: Manasi S. Gangan
and Chaitanya A. Athale (2017) Threshold effect of growth rate on population variability of Escherichia coli cell lengths https://royalsocietypublishing.org/doi/full/10.1098/rsos.160417]

The interface to the program AMTRaK as described in the PLoS ONE report by Chaphalkar et al.

AMTraK: An improved kymograph generator and analyzing program. Writen in a MATLAB using some of the ImageProcessing library toolbox functions. Also available as a bundled program. More details also in our paper:

Chaphalkar AR, Jain K, Gangan MS, Athale CA* (2016) Automated Multi-Peak Tracking Kymography (AMTraK): A Tool to Quantify Sub-Cellular Dynamics with Sub-Pixel Accuracy. PLoS ONE 11(12): e0167620. doi:10.1371/journal.pone.0167620

Rosette plot by Chaitanya Athale (2008) for MATLAB. This simple plotting tool uses the rose plot (popular in circular statistics) to plot frequencies of known period in a circular manner.

Rosette Plot using MATLAB

Rosette Plot using MATLAB

ImageJ batch converter: This code was written because of a constant need to renumber, rename and copy into new formats large clusters of image-files from microscopy. Feel free to use it and let me know if you find bugs. Certainly if you improve on it, do please let me know. [CODE]

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