Co-localisation

In this module, we will cover how to use CellProfiler. We will first learn how to perform simple quantifications of objects of interest in an image. Next, we are going to look at two different approaches to measure co-localisation. Finally, we will have some time to explore the data acquired during the practical session.

Download slides (Optional)

All the slides that will be used in this session are here.

Download demo data

We’re going to be working with some example datasets, which you can download from here.

Fiji macro

• SplitChannels.ijm - Fiji macro for splitting all the multi channel z-stacks in a folder into individual tif images. Takes as input a folder containing the images you want to split, a folder to save the output and the required file extension (e.g., .tif). It requires the Bio-Formats plugin in Fiji.

CellProfiler pipelines

• 01_identify_objects.cppipe - CellProfiler pipeline to perform simple quantifications of objects of interest in an image
• 02_colocalisation.cppipe - CellProfiler pipeline to measure co-localisation with two different approaches