Particle analysis: classifying with respect to size

[Jacqueline Ross]

Dear All,
 
I was wondering if anyone had written a macro or plugin for particle
analysis which automatically uses mean individual particle size to
determine and classify objects as being greater than one particle.
 
What I mean is that sometimes it's not possible to segment out
individual particles properly even with using tools such as watershed.
However, the size of the object is such that you know it is due to 2
particles which have merged together.
 
MetaMorph has a method called Integrated Morphometry Analysis which
allows you to classify objects as being individuals or 2, 3, or more
depending on their size.
 
If anyone can suggest a way of doing this in ImageJ, that would be much
appreciated.
 
At the moment, my idea is to find out the mean (+ 2SD, etc.) using
Analyze Particles and then go into Excel to classify them as one or more
but if anyone has a better way of doing this, it would be great.

Kind regards,
 
Jacqui
 
Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/
<blocked::http://www.health.auckland.ac.nz/biru/>  

 

[Gabriel Landini]

On Friday 14 December 2007 06:07:43 Jacqui Ross wrote:
> I was wondering if anyone had written a macro or plugin for particle
> analysis which automatically uses mean individual particle size to
> determine and classify objects as being greater than one particle.

This may help:

http://www.dentistry.bham.ac.uk/landinig/software/classify/classify.html

> At the moment, my idea is to find out the mean (+ 2SD, etc.) using
> Analyze Particles and then go into Excel to classify them as one or more
> but if anyone has a better way of doing this, it would be great.

That would only work depending on 1. the variability of the particle size and
2. the degree of overlap between particles (some particles may not even have
a normal size distribution!).
I do not believe that one should use a canned solution to that problem. You
could estimate which deviation from the mean size corresponds to 2, 3
particles and so on. To do that you can label some images by hand and see at
the size distribution of the particles.

I hope it helps.

G.

[Jacqueline Ross]

Thanks very much for that Gabriel,

Your plugin looks like what I am looking for. I'll give it a run. I hope
you won't mind if I come back with additional questions!

Kind regards,

Jacqui


Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/ 


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Gabriel Landini
Sent: Friday, 14 December 2007 9:26 p.m.
To: [hidden email]
Subject: Re: Particle analysis: classifying with respect to size

On Friday 14 December 2007 06:07:43 Jacqui Ross wrote:
> I was wondering if anyone had written a macro or plugin for particle
> analysis which automatically uses mean individual particle size to
> determine and classify objects as being greater than one particle.

This may help:

http://www.dentistry.bham.ac.uk/landinig/software/classify/classify.html

> At the moment, my idea is to find out the mean (+ 2SD, etc.) using
> Analyze Particles and then go into Excel to classify them as one or
> more but if anyone has a better way of doing this, it would be great.

That would only work depending on 1. the variability of the particle
size and 2. the degree of overlap between particles (some particles may
not even have a normal size distribution!).
I do not believe that one should use a canned solution to that problem.
You could estimate which deviation from the mean size corresponds to 2,
3 particles and so on. To do that you can label some images by hand and
see at the size distribution of the particles.

I hope it helps.

G.

[Dimiter Prodanov-2]

Hi Jacquie,

I agree with Gabriel, without prior knowledge on the size distribution it
will be difficult to classify. With this statement you assume unimodal
distribution.

how many classes do you normally expect? I have an algorithm for
unsupervised classification in 2^n classes. But it is implemented so far
in Matlab.
----------------------
At the moment, my idea is to find out the mean (+ 2SD, etc.) using
Analyze Particles and then go into Excel to classify them as one or more
but if anyone has a better way of doing this, it would be great.

-----------------

Kind regards,

Dimiter

[Jacqueline Ross]

Hi Dimiter,

Thanks for your reply. I agree that you have to get some initial data in
order to do this.

I intend to do the particle analysis with all particles initially and
then look at the frequency distribution and try to work out from that
which ones are likely to be outliers. I'm looking at cell/nuclei number
but some cells/nuclei are still too close together, therefore presenting
as one object although by eye, you can see from the morphology (and
size!) that there are actually 2 or more contributing to the particle. I
also have a good idea of what the size of the cells/nuclei are.

It would of course be easier if I can easily see clear peaks in the
frequency histogram corresponding to one, two, three particles but it is
a little more complicated than that. I could also choose to exclude
larger particles from the particle analysis initially since I do know
approximately how large the indivdual nuclei are (for example). Then I
could use Gabriel's classification plugin together with that data.

Anyway, I will try out this plugin since it does look like a good
option.

Kind regards,

Jacqui


Jacqueline Ross

Biomedical Imaging Microscopist
Biomedical Imaging Research Unit
School of Medical Sciences
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland, NEW ZEALAND

Tel: [phone] Ext 87438
Fax: [phone]

http://www.health.auckland.ac.nz/biru/ 


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Dimiter Prodanov
Sent: Monday, 17 December 2007 9:29 p.m.
To: [hidden email]
Subject: Re: Particle analysis: classifying with respect to size

Hi Jacquie,

I agree with Gabriel, without prior knowledge on the size distribution
it will be difficult to classify. With this statement you assume
unimodal distribution.

how many classes do you normally expect? I have an algorithm for
unsupervised classification in 2^n classes. But it is implemented so far
in Matlab.
----------------------
At the moment, my idea is to find out the mean (+ 2SD, etc.) using
Analyze Particles and then go into Excel to classify them as one or more
but if anyone has a better way of doing this, it would be great.

-----------------

Kind regards,

Dimiter

[saucedap]

Hello Jacqueline Ross

I have the same problem, you found a way to solve Particle analysis: classifying with respect to size.

Thank you for your attention.

Patricio

[Jacqueline Ross]

Hi Patricio,

I assume that you have found an old message of mine from the archives since you are addressing me directly.

If you want to classify based on size, you could try the Classify Particles plugin http://www.mecourse.com/landinig/software/classify/classify.html written by Gabriel Landini.

Another option is to use the BioVoxxel Toolbox - Advanced Particle Analyzer provided by Jan Brocher: http://fiji.sc/BioVoxxel_Toolbox#Advanced_Particle_Analyzer

I have used both methods with success.

Kind regards,

Jacqui


Jacqueline Ross
Biomedical Imaging Microscopist
Biomedical Imaging Research Unit 
School of Medical Sciences 
Faculty of Medical & Health Sciences
The University of Auckland
Private Bag 92019
Auckland 1142, NEW ZEALAND

Tel: [phone]
Fax: [phone]

http://www.fmhs.auckland.ac.nz/sms/biru/


-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of saucedap
Sent: Wednesday, 11 June 2014 8:02 a.m.
To: [hidden email]
Subject: Re: Particle analysis: classifying with respect to size

Hello Jacqueline Ross

I have the same problem, you found a way to solve Particle analysis:
classifying with respect to size.

Thank you for your attention.

Patricio




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[gankaku]

Hi Jaqueline, hi Patricio,

In addition to the "Advanced Particle Analyzer", the "Shape Desciptor Maps"
from the BioVoxxel Toolbox might also assist you in getting an idea about a
potential classification according to shape descriptors.

I hope that in near futur I will find the time to rewrite the Advanced
Particle Analyzer as plugin to also make it recordable, easy applicable to
stacks and extend it further.

cheers,
Jan


2014-06-12 8:29 GMT+02:00 Jacqui Ross <[hidden email]>:

> Hi Patricio,
>
> I assume that you have found an old message of mine from the archives
> since you are addressing me directly.
>
> If you want to classify based on size, you could try the Classify
> Particles plugin
> http://www.mecourse.com/landinig/software/classify/classify.html written
> by Gabriel Landini.
>
> Another option is to use the BioVoxxel Toolbox - Advanced Particle
> Analyzer provided by Jan Brocher:
> http://fiji.sc/BioVoxxel_Toolbox#Advanced_Particle_Analyzer
>
> I have used both methods with success.
>
> Kind regards,
>
> Jacqui
>
>
> Jacqueline Ross
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland 1142, NEW ZEALAND
>
> Tel: [phone]
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> saucedap
> Sent: Wednesday, 11 June 2014 8:02 a.m.
> To: [hidden email]
> Subject: Re: Particle analysis: classifying with respect to size
>
> Hello Jacqueline Ross
>
> I have the same problem, you found a way to solve Particle analysis:
> classifying with respect to size.
>
> Thank you for your attention.
>
> Patricio
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Particle-analysis-classifying-with-respect-to-size-tp3697736p5008117.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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>

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[saucedap]

Hi Jacqui

Sorry for late reply
 
Thank you very much for your time, your suggestion was helpful.

Best regards. "Have a good day!"


Patricio