Posted by
Dr. Michael DOUBE on
URL: http://imagej.273.s1.nabble.com/Fiji-Drawing-tools-tp5024409p5024418.html
Dear Svenja,
I will reply to a few of Kenneth Sloan's points below. Good luck with the Master's thesis!
On 28/01/2021 02:23, Roosch, Svenja wrote:
Hello everyone,
thanks so much for all your interesting answers. Since the deadline of my master thesis is getting closer, I am trying to do several thing at a time, which - as usual - does not work. I hope to be able to return to this interesting discussion in a few days, or possibly after Febuary 15th. đ Then I will hopefully be able to respond in the detail that is necessary.
Best wishes
Svenja
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Gesendet: Mittwoch, 27. Januar 2021 15:29
An:
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Betreff: Re: Longest axis/minimum containing sphere of 3D object? Interruption
Please excuse my interruption however may I suggest simply orient the image on your screen, take a screenshot (Plugins > Utilities > Capture image). Then set the Analysis to measure the long and short Feret axis on the image?
Just asking,
Bob
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From: Kenneth R Sloan<mailto:
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Sent: Wednesday, January 27, 2021 8:49 AM
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Subject: Re: Longest axis/minimum containing sphere of 3D object?
I agree that this is the right way to characterize âlongest axisâ.
But... the OP did ask for Diameter, which is not the same thing.
Diameter is tricky in 3D. Is thickness required? Then Local Thickness should be used. If longest caliper diameter is required then Feret Diameter is the thing. BoneJ's Particle Analyser does this in 3D via point-to-point brute force. It is pretty slow if the surface mesh is large (maybe a candidate for acceleration with GPU via CLIJ or similar, or just a better algorithm).
Also, I have always been suspicious of methods that find eigenvectors and
eigenvalues and then multiply by a magic constant. This last step has too
many assumptions about the distribution of input points.
Yes for sure, but I don't know what you mean by 'magic constant'. If the particle is roughly ellipsoidal or can be represented by a simple convex hull pretty well ('blob'-shaped) then eigenvalues (and vectors) can represent it OK. Converting from eigenvalues (lambda) to ellipsoid radii (r) in real units is trivial as r = 1 / sqrt(lambda) (assuming / approximating ellipsoid geometry of the blob). It's also possible to fit an ellipsoid to the surface mesh, to arrive at similar estimates.
If the particle is concave, perforated, or otherwise not very blob-like then it should not be approximated as an ellipsoid using these methods.
If the OP still wants Diameter, my opinion is that:
A) minimum enclosing circle is not quite correct,
B) I would find the 3D Convex Hull and then use the obvious brute force
method of finding the Diameter
Both of these appear to require code that goes beyond existing âoff the
shelfâ methods. I suppose that B could be done in the macro language, but
my personal preference would be Java.
B - without the convex hull step - is an option in the Particle Analyser.
Dear Svenja,
Maybe the 3D imageJ Suite (3D ImageJ Suite - ImageJ<
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3D ellipsoid fitting [ImageJ Documentation Wiki] (list.lu)<
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fimagejdocu.list.lu%2Ftutorial%2Fplugins%2F3d_ellipsoid&data=04%7C01%7C%7C4398469693fd43ee50c008d8c2ca5601%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637473521566721277%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=czcNDrS365D1I3ns8iWnSkZ8QUWjAeN3S6hHe4raYk4%3D&reserved=0><
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Manager [ImageJ Documentation Wiki] (list.lu)<
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Best wishes
Kees
Dr Ir K.R. Straatman FRMS
Advanced Imaging Facility
University of Leicester
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Sent: 26 January 2021 09:03
Subject: Longest axis/minimum containing sphere of 3D object?
Hello everyone!
I have a stack of binary images that is to be interpreted as a 3D image. I
have background (in black) and one irregular-shaped object in it (the model
of a soil aggregate). I now want to know the longest axis of this object.
I thought the easiest way would be to let a function find the smallest
containing sphere and take the diameter. I am aware that in BoneJ, there is
a function that allows to find an optimal sphere based on points that are
marked by hand. This is, however, not quite what I need and I hope to find
a solution without too much manual work, since actually, I have a bit more
than one stack. Is anyone aware of a function that can do that?
Another way might be to use the 3D Convex Hull package that can find me
the vertices of a convex hull of a 3D object. Does anyone have an idea how
to find the largest pair-wise distance between them in ImageJ? Or is this
something that's better done with another program?
Any hint is appreciated. Thanks in advance!
All the best,
Svenja
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-Kenneth Sloan
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