Black borders with CorrectIllumination


I’m trying to correct the illumination on my images using the CorrectIllumination_calculate module. I’m using the background option of this module but I always get black borders on the bottom and at the right of the Illumination correction function. I tried different settings but the black borders are always there. I notice the black border size decrease if I decrease the block size (it’s now set to 60) but never disappear. I’m doing the correction on each image (the illumination pattern change between pictures…). I haven’t really play with the smoothing for now as I would like to correct this problem before.
Can somebody know how I could remove this ? Did I miss something ? I sent an image of a function I got (median_filter and artifacts to be smoothed at 100).
Thank you,

Hi Daniel,

Can you upload an example image, plus the pipeline that you used to create the illumination correction function?


Hi Mark,
I uploaded the pipeline (it contain only the illumination correction for now…).
The pictures I sent was created from the AnxV image. I didn’t really work on the hoechst for now.
I don’t know if it’s important but the images were rescaled. They were 12 bits images saved in 16 bits so I rescaled from 0,0.0625 to 0,1.

Thanks for your help.

[attachment=2]CorrectIllum_PIPE.mat[/attachment][attachment=1]GQ-Hoechst - n0000001.tif[/attachment][attachment=0]GQ-Alexa647 AnxV - n0000001.tif[/attachment]

CorrectIllum_PIPE.mat (886 Bytes)

Hi Daniel,

I took a closer look at your images and it turns out that the bottom-most and right-hand pixels of the image all have the same low value (intensity = 5024) which is the minimum value of the entire image. The attached image shows the bottom-right corner of one of your images in which the pixels equal to 5024 are colored white.

Since the background method looks for the lowest value in each block (60 x 60 in your case), the blocks on these edges get filled in with this value (which then gets smoothed a bit). You may want to check your image acquisition to see if this is expected behavior.

How this helps!

Wow, thanks a lot for your help Mark,

I don’t think I would have figured this by myself…
I just crop the last bottom and right pixels of my images and I completely lost the black border in my illumination function. These pixels came from the software we are using for our image acquisition.

Thanks again,