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3D shape descriptors

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3D shape descriptors

Hanna_SN
Dear all,

I am new to image j. I need to somehow characterize shape of particles segmented from 3D image stacks. Unfortunately I can't find any suitable plugin and I don't have a knowledge to write one myself. I would be very grateful if someone could suggest me any plugin or a way to calculate shape descriptors such as roundness or circularity for image stacks.

Best regards,
Hanna
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Re: 3D shape descriptors

Michael Doube
Dear Hanna:

There is a Particle Counter plugin that might help.
http://rsb.info.nih.gov/ij/plugins/track/objects.html

but it goes a bit slow and doesn't do surfaces, so I'm working on making it a bit more 3D. Watch this space!
Or, check it out at github

http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/ParticleCounter.java

Mike
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Hanna_SN [[hidden email]]
Sent: 28 December 2009 08:46
To: [hidden email]
Subject: 3D shape descriptors

Dear all,

I am new to image j. I need to somehow characterize shape of particles
segmented from 3D image stacks. Unfortunately I can't find any suitable
plugin and I don't have a knowledge to write one myself. I would be very
grateful if someone could suggest me any plugin or a way to calculate shape
descriptors such as roundness or circularity for image stacks.

Best regards,
Hanna
--
View this message in context: http://n2.nabble.com/3D-shape-descriptors-tp4222907p4222907.html
Sent from the ImageJ mailing list archive at Nabble.com.
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Counting cells

hemangi
I am trying to count cells in an image by two ways and then co
Hi All,

I am trying to count cells in an image by two ways and then compare the results.
First, I used cell counter plugin and got all cells numbered.
Then, I used 'analyze particles'.
Can I get the summary window to show both:  ellipses from 'analyze particles' and numbers from the cell counter window?
I got it once, but can't get the similar result again!
Would someone please help me?

Thanks,
Hemangi.


 



________________________________
From: "Doube, Michael" <[hidden email]>
To: [hidden email]
Sent: Mon, December 28, 2009 11:40:18 AM
Subject: Re: 3D shape descriptors

Dear Hanna:

There is a Particle Counter plugin that might help.
http://rsb.info.nih.gov/ij/plugins/track/objects.html

but it goes a bit slow and doesn't do surfaces, so I'm working on making it a bit more 3D. Watch this space!
Or, check it out at github

http://github.com/mdoube/BoneJ/blob/master/src/org/doube/bonej/ParticleCounter.java

Mike
________________________________________
From: ImageJ Interest Group [[hidden email]] On Behalf Of Hanna_SN [[hidden email]]
Sent: 28 December 2009 08:46
To: [hidden email]
Subject: 3D shape descriptors

Dear all,

I am new to image j. I need to somehow characterize shape of particles
segmented from 3D image stacks. Unfortunately I can't find any suitable
plugin and I don't have a knowledge to write one myself. I would be very
grateful if someone could suggest me any plugin or a way to calculate shape
descriptors such as roundness or circularity for image stacks.

Best regards,
Hanna
--
View this message in context: http://n2.nabble.com/3D-shape-descriptors-tp4222907p4222907.html
Sent from the ImageJ mailing list archive at Nabble.com.

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Updated 3D particle counter

Michael Doube
In reply to this post by Hanna_SN
Hi all

In response to requests here and in the real world (if university counts
as the real world), I've made a few adaptations to the 3D Object Counter
so that it can do a few fancy new tricks:

1) Label particles a lot faster.  Recursion in particle labelling is
reduced and multithreaded so that jobs on big stacks end before our
universe does.

2) Euler calculations for each particle, returning Euler characteristic,
number of cavities and holes per particle.

3) Surfaces and surface area estimates of each particle

4) Ellipsoid fitting, so that people can work out the
oblate/prolate/scalene/spheroidal nature of their particles

5) Moments of inertia and orientation of principal axes

6) Thickness of each particle

7) Display graphical results in a 3D Viewer window, where you can select
each numbered particle

8) Display numerical results in a Results table

All calculations are done in 3D, and voxel methods are used except for
surface area and ellipsoid fitting, which use the results of Bene's
surface mesher.

At the moment it works on binary stacks, and I've only tested it on the
images I have to hand, so your feedback would be very valuable.

The plugin is part of BoneJ, which is available here:
http://doube.org/bonej.html

Once installed, there is a new item in Plugins->Analyze->Particle Analyser.

Have a happy new year,

Michael

--
Dr Michael Doube  BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London  SW7 2AZ
United Kingdom
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Re: Updated 3D particle counter

David Webster
Michael,

Have you updated your 2D Circle Fit plugin for ellipses yet?

David Webster

On Wed, Dec 30, 2009 at 11:49 AM, Michael Doube <[hidden email]>wrote:

> Hi all
>
> In response to requests here and in the real world (if university counts as
> the real world), I've made a few adaptations to the 3D Object Counter so
> that it can do a few fancy new tricks:
>
> 1) Label particles a lot faster.  Recursion in particle labelling is
> reduced and multithreaded so that jobs on big stacks end before our universe
> does.
>
> 2) Euler calculations for each particle, returning Euler characteristic,
> number of cavities and holes per particle.
>
> 3) Surfaces and surface area estimates of each particle
>
> 4) Ellipsoid fitting, so that people can work out the
> oblate/prolate/scalene/spheroidal nature of their particles
>
> 5) Moments of inertia and orientation of principal axes
>
> 6) Thickness of each particle
>
> 7) Display graphical results in a 3D Viewer window, where you can select
> each numbered particle
>
> 8) Display numerical results in a Results table
>
> All calculations are done in 3D, and voxel methods are used except for
> surface area and ellipsoid fitting, which use the results of Bene's surface
> mesher.
>
> At the moment it works on binary stacks, and I've only tested it on the
> images I have to hand, so your feedback would be very valuable.
>
> The plugin is part of BoneJ, which is available here:
> http://doube.org/bonej.html
>
> Once installed, there is a new item in Plugins->Analyze->Particle Analyser.
>
> Have a happy new year,
>
> Michael
>
> --
> Dr Michael Doube  BPhil BVSc PhD MRCVS
> Research Associate
> Department of Bioengineering
> Imperial College London
> South Kensington Campus
> London  SW7 2AZ
> United Kingdom
>
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Re: Updated 3D particle counter

Michael Doube
Hi David

Thanks for reminding me.  I tried and failed (at least, gave up for the
time being to do other things).

Mainly I get tired porting from MATLAB because MATLAB handles matrices
very neatly while Java is somewhat more circuitous, so there's a lot of
tiresome array iterating to do what can be done in 3 characters in an
m-file.

If anyone is interested, the methods I'm in the middle of porting are this:
http://www.mathworks.co.uk/matlabcentral/fileexchange/22683-ellipse-fit-taubin-method
and this:
http://www.mathworks.co.uk/matlabcentral/fileexchange/22684-ellipse-fit-direct-method

Ping me again sometime soon and I'll have another go.

Right, time for tea.

Mike

David Webster wrote:

> Michael,
>
> Have you updated your 2D Circle Fit plugin for ellipses yet?
>
> David Webster
>
> On Wed, Dec 30, 2009 at 11:49 AM, Michael Doube <[hidden email]>wrote:
>
>> Hi all
>>
>> In response to requests here and in the real world (if university counts as
>> the real world), I've made a few adaptations to the 3D Object Counter so
>> that it can do a few fancy new tricks:
>>
>> 1) Label particles a lot faster.  Recursion in particle labelling is
>> reduced and multithreaded so that jobs on big stacks end before our universe
>> does.
>>
>> 2) Euler calculations for each particle, returning Euler characteristic,
>> number of cavities and holes per particle.
>>
>> 3) Surfaces and surface area estimates of each particle
>>
>> 4) Ellipsoid fitting, so that people can work out the
>> oblate/prolate/scalene/spheroidal nature of their particles
>>
>> 5) Moments of inertia and orientation of principal axes
>>
>> 6) Thickness of each particle
>>
>> 7) Display graphical results in a 3D Viewer window, where you can select
>> each numbered particle
>>
>> 8) Display numerical results in a Results table
>>
>> All calculations are done in 3D, and voxel methods are used except for
>> surface area and ellipsoid fitting, which use the results of Bene's surface
>> mesher.
>>
>> At the moment it works on binary stacks, and I've only tested it on the
>> images I have to hand, so your feedback would be very valuable.
>>
>> The plugin is part of BoneJ, which is available here:
>> http://doube.org/bonej.html
>>
>> Once installed, there is a new item in Plugins->Analyze->Particle Analyser.
>>
>> Have a happy new year,
>>
>> Michael
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