Unless your imaging facility is in a clean room (and you never touch it), from time to time, we all end up with unsightly splotches on our transmitted light images. The best fix for this is to clean the microscope but sometimes you just have to do what you can with what you’ve got.
Thankfully there’s a fairly easy way to correct it post-acquisition. Let’s Flat-field correct!
A lot of work we do at the CCI uses scanning confocal microscopes, which have the advantage that the operator can pick the number of pixels in X and Y that will make up the final image.
For camera-based systems this is a less simple endeavour as the array of the CCD chip is fixed. For this reason, we may want to downsample or bin our images. In this post we’ll cover a bit of theory and details on how (and why) to bin your images.