Dear Sir or Madam,
I am writing to ask for your advice about the problems our laboratory encountered during the processing of the ImageStream data with CellProfiler.
First question. This article provided us an example of user-friendly solution for working with CellProfiler, when .cif file is uploaded directly to CellProfiler. Unfortunately, we could`t do this with ImageStream .cif file Could you explain how we can make it?
Second question. Now we process Image Stream data after image extraction from .cif file. Our purpose is to count black dots on cell’s surface. Unfortunately, function IdentifyPrimaryObjects in CellProfiler allows to count only light objects on dark background. Threshold in CellProfiler does not allow me to distinguish black dots. Due to this I have to invert colors manually with python script. Is there in CellProfiler possibility to invert colors in image or count dark objects on light background?
Third question. In some articles and on YouTube I saw examples of image classification using machine learning with CellProfiler Analyst. Could you tell me please is CellProfiler Analyst able to count black dots on cells using machine learning? Could you explain me how to do this task if it is possible?
I use CellProfiler 3.1.5.
I look forward to your reply.
Ivan Kotov, laboratory of nanobiotechnology, MIPT