Image analysis of colony growth

© 2021 Tom Röschinger. This work is licensed under a Creative Commons Attribution License CC-BY 4.0. All code contained herein is licensed under an MIT license

In this notebook we are going to use microscopy data of bacteria to determine their growth rate. In order to do that, we took images of the same colony over a period of about 1-2 hours.

The first step is to set the path to the data set.

Let's load an image into memory.

As we can see, an image is just a two dimensional array of intensities. We can look at an image by using the imshow function of pyplot. Since we only have one channel, we will simply use a grey scale to show the image. Some images can have multiple channels in order to image different things at the same time (such as fluorescent proteins with varying emission wavelengths).

A good step is to normalize the intensity values, such that they range from 0 to 1. This allows us to compare different images to each other.