ScanningManager software application - Unix
For controlling image acquisition by an array of scanners.
source code (GitHub)
Materials
ScanningManager software application - Windows
For controlling image acquisition by an array of scanners.
source code (GitHub)
Pipeline for detecting DNA inversions in sequencing data
This pipeline's purpose is to use Whole Genome Sequencing (WGS) data in order to detect genomic inversions in the genomes of bacteria and calculate their prevalence in the population. It is a supplementary material to the paper "Systematic Identification and Quantification of Phase Variation in Commensal and Pathogenic E.coli" (Goldberg, A. et al., Genome Medicine 2014).
ScanLag - TimeLapse analysis software application (Matlab)
For the analysis of images and extraction of colony appearance data
source code (GitHub)
Automated detection and analysis of growing E.coli bacteria
The movie shows the tracking procedure, on top of the YFP raw images (here represented
in gray scale). Each cell is assigned a color automatically. Divisions are automatically detected and daughter cells identified. The algorithm builds a tree of the progeny of each cell.
Growth of hipQ bacteria in a microfluidic chamber
Bacteria are first exposed to growth medium and grow in the narrow grooves. Ampicillin treatment (marked "Amp") results in the massive lysis of cells. After the ampicillin is washed out, persister cells grow and divide. Note that the persister cells were are slowly growing before, during and after the ampicillin treatment. Time between consecutive frames: 4 minutes during the first growth medium period and the first two hours of the ampicillin treatment; 11 minutes during the end of the ampicillin treatment and the second growth period.
Time-lapse microscopy of mammalian cells
L1210 lymphoblasts expressing the Fucci cell cycle markers were image under the microscope to follow the duration of the cell cycle in each cell.
http://www.nature.com/nature/journal/v519/n7544/full/nature14318.html