Could anyone shed a light on how the CorrectIllumination function is calculated between ‘each’ and ‘all’?
I am understanding the function as:
- choosing ‘each’ means that the illumination function is only calculated based on one image that is being processed.
- choosing ‘all’ means that the illumination function is calculated based on all images in the project.
The reason I am asking this question is that whenever I choose ‘all’ to calculate the function, something strange happens.
The first image has no issues.
The second image has black spots that resemble where the objects were in the first image.
The third image has black spots that resemble where the objects were in both first and second images.
And it repeats throughout the list of images.
In this case, the objects exclusively mean cell bodies of neurons in my neuron images.
I do have a pipeline and the output images that show black spots in the post here:
If I am understanding the function correctly, I would want to calculate it based on all images to best eliminate the background in a data set.
However, these black spots force me to choose ‘each’ instead of ‘all’.
Any advice would be greatly appreciated.