How to isolate fibers in picture by cell profiler

I am trying to isolate the fibers and exclude the cluster, but after using threshold module, the picture loses its reality and become over-exposed. The instruction of threshold said it helps to remove some area that has more intensity and I was going to remove the cluster because they are usually very bright area. But mine seems not work as I expect. Anyone familiar with threshold module?


A picture would help us understand the situation.

Hi @xxl,
Welcome to the community!
As Mathew suggested, could you upload your pipeline and some sample images, so we can help you better?

Meanwhile, you could check some of the tutorials and examples on the website.

C5-2_z44_ch02.tiff (1.0 MB)
I just hope to remove some clusters and may contain a bunch of fibers or noise and get a clean actin picture. What module I should use in cell profiler?


It seems you want to remove the oversaturated pixels from your image, one of the ways you can do this is by thresholding and masking your image:
You can use “Threshold” module to detect the high intensity pixels (you can find the pixel intensities by hovering over each pixel and in the bar at the bottom right of your window, you’ll see the intensity). For example, you can set the threshold to be between 0.8 to 1 to pick the higher intensity pixels.
You then can use this thresholded image to mask your image, you want to invert your mask, so your final image has all the other areas, except the clusters and high intensity areas.
Then by using “IdentifyPrimaryObjects” module you can detect the fibers. You may need to enhance some features of the image by using “EnhanceOrSupressFeatures” before detecting the objects.

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