ScanningManager software application - Unix
For controlling image acquisition by an array of scanners.
source code (GitHub)
For controlling image acquisition by an array of scanners.
source code (GitHub)
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).
For controlling image acquisition by an array of scanners.
source code (GitHub)
The mother-machine design (Wang et al. Current Biology 2010) was adapted for the continous monitoring of single-cell divisions in L1210 mammalian cells (Pearl Mizrahi et al., Cell Cycle 2017)
For the analysis of images and extraction of colony appearance data
source code (GitHub)
Test images from the zip file here (the zip preserves the correct time of the image), where you will also find an updated manual.
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.
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