Image Sequence - Measure a Voume of aggregate

I would like to measure the volume of the aggregate (without the round pipe - see picture) from a image sequence. What is the procedure?
Is there a way to cut the round pipe away before?

Thanks in advance.

Have a lookt at the 3d Objects Counter:

or the BoneJ implementation:

To measure objects within a region of interest see also this answer of @ThomasBoudier in the mailing list:

Hi @NeroDB90

You could try to subtract a minimum-projection from each of the stack-slices. If the pipe does not move and the aggregate is surrounded by some black background you could remove the pipe like this.

After that you can perform standard thresholding since your images are really clean.

If your pipe is always touching the edge and the particles of interest are not, you could use the “exclude on edges” option in the 3D OC or BoneJ to get rid of the pipe.

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Tanks for you advices,
I tried out today the 3D manager, but Fiji gives me allways a mistake when I try to open “3D Manager”:

Im not sure what the problem is?
Also the ROI doesnt work - in the 3D Viewer is still the pipe?!

The same with BoneJ

There is allways a problem with Java 3D!

Do you have any ideas?

See here:

To exclude the ring as addition to the before mentioned recipes and if you have a static ring you could also clear the outside of all images in the stack with an oval selection (in you example choose black as color before):

The class did not find Java3D (javax/vecmath/Color3f)
Please call Plugins>3D Viewer to install

Hmm, that plugin is from the 3D ImageJ Suite, right? It looks like it requires the old Java 3D, from before the update to Java 8 (right, @ThomasBoudier?). See this guide for some details. The gist is that you will need to use the old “Java 6” version of Fiji with the 3D ImageJ Suite until it can be updated to use the new APIs. Sorry for the inconvenience.

Hi @NeroDB90 and @ctrueden,

Yes, 3D suite uses the “old” version of 3DViewer, so usually I do a very bad thing : I replace the 3DViewer plugin from Fiji by the “old” one found in Benjamin´s website :
However I would be happy to update 3DManager to interact with the new 3DViewer.



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@ThomasBoudier Would you like me to file a pull request against ?

Hey to ALL,
thanks for your reply, it was really really helpful. I downloaded a old version of Fiji and now it seems to be, that it works - THANKS

Hey Bio7,
but if I do it in this way, I have to do this for each image or (and I have a image sequence of more then 800 pictures). Is there no way to cut it away like “crop” but like a circle?


If you have a stack or import your images as a stack:

File->Import ->Image Sequence

(Or simply drag the image folder on the ImageJ toolbar)

then it will process (clear) all slices if you confirm the dedicated dialog for the action!

hi @ctrueden,

Yes we can do that, I am not a expert in the github things but let us try, anyway I will need help to update 3DManager to use the new 3DViewer.



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