Correct illumination



The module “correct illumination”, does it somehow calculate the offset?
If this is the case, would it perhaps be good to give some images of the same objects but different time points? For a perhaps more precise calculation?




Hi Dominik,

Yes, the CorrectIllumination_Calculate module does produce a correction function which can either be applied (using CorrectIllumination_Apply) by dividing the image by the function or by subtracting it, in which case it is essentially an offset.

Since CorrectIllumination_Calculate optimally estimates the function based on set of images taken under the same experimental conditions with the same optics, the best case scenario is provide it with as many images as possible. If this is true for your case (and it sounds like it is), then estimating a correction function from a time-lapse series should work.

You can make a separate pipeline with the CorrectIllumination_Calculate module, setting the appropriate parameters to ‘All’ and ‘Pipeline’ (see the Help for details on what these values mean). Then, you can run it on all the time point images to produce a final correction function which you can save as a .mat file. Lastly, make an analysis pipeline in which you load this correction image and apply to each image in turn using CorrectIllumination_Apply. If you have multiple channels/wavelengths, you will need to generate a correction function for each one.

I hope this helps you get started!