Image segmentation

Hi there,

I met a problem in image segmentation.

I want to segment area as part 1 and part 2 from the background (such as part 3). However, when I used threshold, the resulted image is as follows.

The background will affect the thresholding that part 1 cannot be separated from background (e.g. part 3).

I really appreciate that if anyone can help me with this problem. The original image is uploaded.

Thank you,


First of all, to get better results, you should try to improve the acquisition if possible:

  • Change the acquisition settings to cover the full dynamic range of the signal in the image. The image you uploaded seems clipped/saturated at the bright spots.
  • Choose an appropriate file format to save your files. See the wiki section about why to a avoid lossy compression file formats.

To segment the different areas, you can try machine learning, e.g. the Trainable Weka Segmentation plugin. See this other discussion on the forum for some more explanations.

Here’s what I got when quickly trying to label the areas you described and then training the classifier:

Alternatively, you can try other software such as ilastik.


Thank you, I’ll try to save the image as Tif format and process it.