Team:TU Eindhoven/Modeling/Bacterial Cell Counter

Bacterial Cell Counter

When photos of the microfluidics results are taken, the droplets and the cells in the droplets have to be counted. In order to have reliable results this has to be done on a large scale. To make it possible to analyses large numbers of photos a computer program has been made to do the counting. To give a better visualization of the process, a step by step analysis of an image is given below.

The program has the following steps: find and count the droplets, then find and count the cells in the droplets and finally create a histogram of the results (number of droplets with 0 cells, with 1 cell, with 2 et cetera). By adding up the histograms of multiple images you get a view of how the cells are divided over the droplets.

Droplet Detection

To detect the cells EdgeDetect (a function of Mathematica using gradient methods) is used followed by a dilation to make the edges clearer.

This results in clusters of pixels, all the pixels that are connected with only black pixels. The program then looks for the clusters bigger than 2000 pixels and smaller than 6000 pixels.

Handle with Parameters of the Droplets Detection

Bibliography