I am running a set of images in CellProfiler with Illumination Correction modules.
Whenever I set the parameters in “CorrectIllumination Calculate” as:
- Calculate function for each image individually, or based on all images?: All: Across cycles
There are black spots in all images after the first image.
The position of black spots correlates to the position of objects in the previous images.
For example, the second image has black spots where the objects are in the first image and the third image has black spots where the objects are in the first and second images, and so on and so forth.
Here is my pipeline.
illum_corr_all_blackness.cppipe (10.8 KB)
Here are my images.
test_B1_grayscaled_corrected_contrast.tif (8.0 MB)
test_B4_grayscaled_corrected_contrast.tif (8.0 MB)
test_B5_grayscaled_corrected_contrast.tif (8.0 MB)
test_B6_grayscaled_corrected_contrast.tif (8.0 MB)
Any advice would be greatly appreciated!!
Have a great weekend.