In the menu
Analyze, the Analyze Particles... is the headquarters of all the various measurements you can do. Here is a brief explanation of the main features of this dialog window.1. Presentation
Note: The main features are described in the ImageJ User Guide in section 30 [Link]
2. Use of Include Holes
The Include Holes is always a mysterious option. Just look at the following binary image (Fig. 2). This test image contains three types of objects (rings, disks, and squares).  |
| Fig.2: Test image |
A ring (area: 512px) is smaller than a disk (area: 1020px), because a ring is a hollow disk. However, if we fill the inner part of the ring and if they have exactly the same shape, the areas must be identical. Now, run again the Analyze > Analyze Particles... and check the Include Holes option, we get...
... exactly the same areas allowing us to conclude that these two structures are perfectly superimposable.
3. Use of Analyze > Analyze Particles... to create a mask
The choice of the display mode Show is very often just a matter of choice — in my case, I always use the Show Outlines — but sometimes it is very convenient to choose a specific display. Here is an example...In the test image of Fig.2, we are only interested by disks and squares, the rings are "noisy" structures. Rather than doing complicated filtering, mathematical morphology operations, the simplest way is to remove them by using the
Analyze > Analyze Particles...In this image, the area of the rings (area: 512) is smaller than those of the other objects (area: 1020). Thus, by selecting a size range of
700-Infinity and choosing a display mode Show: Masks (Fig.3), you get a cleaned representation of the test image ... and the rings are gone. |
| Fig.3: Use of the Analyze Particles... to remove objects in the input thresholded image. |
You can now measure something on the remaining objects...
Hope that helps.
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