What is the optimal block size of images?

hello,CellProfiler staffs! I am a rookie user of CellProfiler and have utilized this sotfware just a few days.Now i get trouble with illumination correction:how to figure out the optimal block size of images?i have googled for the explanation of this parameter on the forum and website,however i can’t still understand relative answers,for example,“a block should large enough to cover some background”.How can i determinate the best parameter as “large enough”?
i attached my parameter settings and the original picture.The scale bar (not show on the original picture) is 50μm.
my_illumination_correction.cpproj (403 KB)




Hi,

Your image does not seem to be uploaded. Can you try again?

If your cells/objects of interest are not confluent, i.e. they have some background pixels visible, then you can use the Background method. So imagine that a square passes over the image pixel-by-pixel. What is the smallest square you can use, such that every location would always include a “background” pixel? This is usually around the size of your cells if there is some spacing between them. If they all touch, then you should use a different method for illumination correction (“Regular”).

But please post an image. And are you sure you really need illumination correction? There are many different ways you might want to normalize your image and they can radically affect your results (positively or negatively!), so be careful.

David

[quote=“davidlogan”]Hi,

Your image does not seem to be uploaded. Can you try again?

If your cells/objects of interest are not confluent, i.e. they have some background pixels visible, then you can use the Background method. So imagine that a square passes over the image pixel-by-pixel. What is the smallest square you can use, such that every location would always include a “background” pixel? This is usually around the size of your cells if there is some spacing between them. If they all touch, then you should use a different method for illumination correction (“Regular”).

But please post an image. And are you sure you really need illumination correction? There are many different ways you might want to normalize your image and they can radically affect your results (positively or negatively!), so be careful.

David[/quote]

It seems that the public links which created by Microsoft Onedrive doesn’t work well ,so i reuploaded my origin picture again using attachment.