if you can mathematically define “background” of your images, I may be able to tell you how to set it to zero!
Hello Dear Harbie,
Thank you for reply,
I am new to CellProfiler, I don’t know how to mathematically define background to zero if you could tell me provide me any material or links it would be of a great help.
these are your images. You know how they were acquired, you know what is of interest and what is not. So how do you expect that I can tell you what you consider background and how to define it?
This task is entirely your’s and it has nothing to do with software.
(Personally I’m not acquainted with CellProfiler.)
define background to zero
I didn’t write this. I wrote
mathematically define “background” of your images
This means that you have to formally tell what you consider background and what you consider foreground. Because computers understand only formal, i.e. in the end mathematical definitions, we need those.
Here is a possible result
that is mathematically defined but I have no idea whether it suits your needs.
The Image was acquired by FESEM (Field Emission Scanning Electron Microscope)
If I did the image professing in MATLAB code I can define the background pixel intensity to zero but i dont know how it is done in CellProfiller tool.
May I know how did you obtain the Image you have attached? Are you using the cell profiler tool or any other tool
Thanks and Regards.
If you know how to do it in MATLAB then tell us exacly how by posting the code!
As I’ve written I have no idea about CellProfiler, so I can’t help with finding a CellProfile-based solution.
I am looking different method.
I would surely share my final results and procedure in details when I am done
Thanks and Regards,
If you know specific value below which is a background, you can simply subtract that value from the image (see https://forum.image.sc/t/cellprofiler-subtract-a-fixed-value-from-images/22478/2).
If you don’t know the background value, you may want to test Threshold module, to separate background from foreground. Output of that module is mask image by which you can multiply your original image (see ImageMath module) to get “completely dark background”.
I fear you haven’t had a look at the image, that can’t be treated as you describe it.
The image has an extremely low S/N-ratio and requires much more processing than background subtraction or thresholding.
Furthermore, it is unclear to me whether background subtraction or division is adequate because I’m not an expert concerning FESEM.
I agree, the image is kinda tricky and it requires some additional processing steps. However, the original question was how to convert background to 0 in CellProfiler. And
Thus I answered the asked question.
I think you indirectly refer to a language problem the OP seems to have …
(At least my interpretation of statements differs from yours.)
Besides, the OP appears not to be aware of principal limits of what he likes to obtain, but we shall see when the OP presents the results.
Thank you for the suggestion I will look into the steps you suggested me.
We are looking forward to seeing your results!