I have just started to use ImageJ, so my apologies of my request has been asked previously or is ridiculously obvious to experienced users.
I am using Imagej 1.51f in Fiji. I have reasonably well managed to segment an image, using the Morphological Segmentation utility in the MorpholibJ plugin, a small portion of the result is shown above left.
I want to count all of the “basins” that MorpholibJ has created, irrespective of their colour.
In the middle is the same image which I’ve variously tried converting to grey-scale, binary and a binary mask, and threshholding, in order to use the Analyze Particles function in Fiji/ImageJ. However, despite changing the settings in a variety of ways, Analyze Particles produces the result shown on the right, i.e. it does not recognise the segments in the image. I have tried several different outputs from Morphological Segmentation, including masks, with/without dams etc., with no better results.
If anyone can tell me a relatively simple way to count the individual segments / basins, preferably without the conversions / threshholding I should be very grateful. I have a large number of large images to process, therefore manual methods, or any requiring manual intervention are of limited use.
Many thanks in advance.