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.