I am sorry in advance if the problem sounds naïve but I am quite new to ImageJ/Fiji and I have used it before only for some very simple area measurements on pictures with very good contrasts.
I need to measure the area of different carbonate layers with different colours in sections of fossil shells.
From the attached picture, you can notice that the section is characterized by many not-organized layers, that can be grouped in 2 categories:
- “grey layer” - the main matrix of the shell that looks grey with some shadows of blue/yellow
- “white layer” - many white lenticular deposits within the grey layer
What I am trying to measure are:
- the total area of the shell section
- the area of the white layer
- the area of the grey layer (this would just be total – white area)
In this case I having a really hard time with thresholding and extracting both the whole section area and the white patches.
The white of the “white layer” is not so homogenous and I think that it is the main problem. I have already tried improving contrast, various filtering options in ImageJ but without success. I thought that the color contrasts in the image were enough high to get away with it without much processing.
Do you have any advice to process the image or improve contrasts with ImageJ to threshold the total/white areas more easily? Or perhaps is there a better way of doing it (such as using segmentation)?