Black borders with CorrectIllumination

Hi,

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,
Daniel[attachment=0]bckg.jpg[/attachment]

Hi Daniel,

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

Regards,
-Mark

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.
Daniel

[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!
-Mark

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,
Daniel