Subtract Background, RGB to Grayscale problem


Hello. I am a student and I am using this program to count alpha radiation tracks on LR-115 detectors. I’ve encountered a few problems. First, my image is RGB and I need to make it Grayscale. The function does not work and it shows an error that says this picture is already Greyscale. But it is not. Since my .tiff file is bigger than the limit I’ll attach a Google drive link. I didn’t find any image sharing websites to suport .tif files.

The second problem that I’ve encountered is that I can not substract background so that it will be like this: . Also a google drive link.

Note: the second file is processed file of the first file using ImageJ.

Thank you in advance!


For your first error, check your settings in NamesAndTypes- my guess is that you have it set as a Grayscale and not a color image.

For your second, it’d be helpful to know exactly what operations you did to process it in ImageJ, but using the CorrectIlluminationCalculate + CorrectIlluminationApply modules will probably take care of what you need. If not, you may have to pre-process your images through ImageI first before proceeding to count them with CP.


I solved the first error. Thank you for that. I will also try to use CorrectIlluminationCalculate and CorrectIlluminationApply to solve the second one.

In ImageJ I used Substract Background. That is the name of the operation. I saw that Cell Profiler has some of the ImageJ integrated functions but there is not one operation by the name of Substract Background. In ImageJ first thing I did was to Split Channels and to choose Blue processed image. Basically it transformed RGB photo to Greyscale. After this operation I used Substract background so that the entire grey background would disappear and only the black dots would remain. Finally I used a threshold of 200. These are all the operation I used so I could process the first image into the second.

I would like to find a way so that I could use only Cell Profiler to do the operations above + ImageMath (Invert) , IdentifyPrimaryObjects and finaly Export to SpreadSheet. I want to do this just because there are hundreds of images that I need to process and using both ImageJ and CellProfiler would take me like forever.

Thank you for your time.