calculation of the distance between points (gold particles)

[Maria Rubio]

Hello,

I would like to calculate the distance between several gold particles, e.g.
30 particles which are in within an area of 0.03 or 0.06 um2. Is there a way
to calculate that using ImageJ. I know how to do it manually, but I want to
know if there is another way that is less time consuming.

Thanks!

Maria

[David Webster]

Maria,

I don't know if there is a single self contained plugin or macro to do this.
For a manual method, you might try using the line tool. This give the line
length.

For an automated scheme

1. "Process/Binary/Make Binary" to convert your gold particle images to a
binary iumage.

2. "Analyze/Set Measurements" anbd check the "Center of Mass" option.

3. "Analyze/Analyze Particles" will give you a results table with each row
corresponding to a particle. The rows contain the Center of Mass values.

You will then need to write a macro to run thru the rows a pair at a time to
compute the Euclidean distances using the Centers of Mass. I assume this
will be pixels. If so you need to do the conversion to microns. I think,
that there is a way to set the calibration of an image to account for this,
but you will need to look it up, in the online dicumentation.


David

On Fri, Mar 5, 2010 at 1:39 PM, Maria Rubio <[hidden email]> wrote:

> Hello,
>
> I would like to calculate the distance between several gold particles, e.g.
> 30 particles which are in within an area of 0.03 or 0.06 um2. Is there a
> way
> to calculate that using ImageJ. I know how to do it manually, but I want to
> know if there is another way that is less time consuming.
>
> Thanks!
>
> Maria
>

[karo03]

Have a look into the plugin "Delaunay Voronoi". From the Delaunay Triangulation you will get a list of neighborhoods (edges) in the results table. From the coordinates you can calculate the distances (in a macro or in excel).

Regards
Karsten

Am 05.03.2010 um 22:39 schrieb Maria Rubio:

> Hello,
>
> I would like to calculate the distance between several gold particles, e.g.
> 30 particles which are in within an area of 0.03 or 0.06 um2. Is there a way
> to calculate that using ImageJ. I know how to do it manually, but I want to
> know if there is another way that is less time consuming.
>
> Thanks!
>
> Maria

Karsten
[hidden email]

[David Webster]

Karsten,

Hmm! Does "Delaunay Voronoi" does all point pairs? Maria's post wasn't
specific as to which point pairs she would want.

David

On Fri, Mar 5, 2010 at 11:44 PM, Karsten Rodenacker <[hidden email]>wrote:

> Have a look into the plugin "Delaunay Voronoi". From the Delaunay
> Triangulation you will get a list of neighborhoods (edges) in the results
> table. From the coordinates you can calculate the distances (in a macro or
> in excel).
>
> Regards
> Karsten
>
> Am 05.03.2010 um 22:39 schrieb Maria Rubio:
>
> > Hello,
> >
> > I would like to calculate the distance between several gold particles,
> e.g.
> > 30 particles which are in within an area of 0.03 or 0.06 um2. Is there a
> way
> > to calculate that using ImageJ. I know how to do it manually, but I want
> to
> > know if there is another way that is less time consuming.
> >
> > Thanks!
> >
> > Maria
>
> Karsten
> [hidden email]
>

[karo03]

Of course not. But if all distances should be calculated, what could be expected from such a measure?

Karsten

Am 06.03.2010 um 20:24 schrieb David Webster:

> Karsten,
>
> Hmm! Does "Delaunay Voronoi" does all point pairs? Maria's post wasn't
> specific as to which point pairs she would want.
>
> David
>
> On Fri, Mar 5, 2010 at 11:44 PM, Karsten Rodenacker <[hidden email]>wrote:
>
>> Have a look into the plugin "Delaunay Voronoi". From the Delaunay
>> Triangulation you will get a list of neighborhoods (edges) in the results
>> table. From the coordinates you can calculate the distances (in a macro or
>> in excel).
>>
>> Regards
>> Karsten
>>
>> Am 05.03.2010 um 22:39 schrieb Maria Rubio:
>>
>>> Hello,
>>>
>>> I would like to calculate the distance between several gold particles,
>> e.g.
>>> 30 particles which are in within an area of 0.03 or 0.06 um2. Is there a
>> way
>>> to calculate that using ImageJ. I know how to do it manually, but I want
>> to
>>> know if there is another way that is less time consuming.
>>>
>>> Thanks!
>>>
>>> Maria
>>
>> Karsten
>> [hidden email]
>>

Karsten
[hidden email]

[Kenneth Sloan]

On Mar 6, 2010, at 17:41 , Karsten Rodenacker wrote:

> Of course not. But if all distances should be calculated, what could be expected from such a measure?
>
> Karsten
>  

This is not often what most people want these days - but there are several long-established statistical
techniques which start with the measurement of ALL the distances between ALL pairs of points.  Delaunay triangulation
is a relatively new technique (gaining favor sometime in the 1980's or so - during the 1980's I can recall
using both Voronoi/Delaunay based measurements AND all-pairs methods to analyze the packing geometry of photoreceptors in human retina).

Given a histogram of all-pairs distances, it is possible to make inferences about the distances involved in the FIRST ring of neighbors - and also the second, and the third - depending on how regular the arrangement is.


--
Kenneth Sloan
[hidden email]

[karo03]

... interesting thread!
Thank you for your remarks, Kenneth and Jim.

May be it is a bit academic or philosophical, but talking about the set of distances from one selected or designated object to all others or from all objects to all others makes a certain difference.

Assuming that from Maria Rubio not the set of all distances was intended (no designated object), my question was which measure can be extracted from the set of all distances from all to all.

By the way, Delaunay triangulation reflects strongly our visual habits. If we look at a set of objects (points) and try to designate neighbors of one point, we mostly select Delaunay neighbors. I think there is a publication starting from the background skeleton (a generalization of Voronoi) from Fernand Meyer and its relation to visual neighboring of objects.

Karsten
 
Am 07.03.2010 um 02:27 schrieb Kenneth Sloan:

> On Mar 6, 2010, at 17:41 , Karsten Rodenacker wrote:
>
>> Of course not. But if all distances should be calculated, what could be expected from such a measure?
>>
>> Karsten
>>
>
> This is not often what most people want these days - but there are several long-established statistical
> techniques which start with the measurement of ALL the distances between ALL pairs of points.  Delaunay triangulation
> is a relatively new technique (gaining favor sometime in the 1980's or so - during the 1980's I can recall
> using both Voronoi/Delaunay based measurements AND all-pairs methods to analyze the packing geometry of photoreceptors in human retina).
>
> Given a histogram of all-pairs distances, it is possible to make inferences about the distances involved in the FIRST ring of neighbors - and also the second, and the third - depending on how regular the arrangement is.
>
>
> --
> Kenneth Sloan
> [hidden email]

Karsten
[hidden email]

[Gabriel Landini]

On Sunday 07 March 2010, you wrote:
> ... interesting thread!

And after a feeling of deja-vu I found this thread worth reading:

https://list.nih.gov/cgi-bin/wa?A2=ind0705&L=IMAGEJ&P=R7156&I=-3

which includes a macro for the nearest neighbour graph (using the centre of
mass of particles).

https://list.nih.gov/cgi-bin/wa?A2=ind0705&L=IMAGEJ&D=0&I=-3&P=14790

Cheers

G.

[Maria Rubio]

Thanks f ro your discussion.

I'm interested on detecting a change in the distribution of gold particles between control and experimental. My images come from SDS-FRL replica immunolabeling of synapses.
so I think getting the distance between/among the particles I could get the numerical data for later on doing some statistics!!

Best!

Maria


Maria E. Rubio M.D./Ph.D
Department of Otolaryngology
University of Pittsburgh Medical School
BST3 Building
3501 Fifth Avenue #10015
Pittsburgh, PA 15261
Phone: [phone]
Fax: [phone]
e-mail: [hidden email]

On Mar 7, 2010, at 5:39 AM, Gabriel Landini wrote:

> On Sunday 07 March 2010, you wrote:
>> ... interesting thread!
>
> And after a feeling of deja-vu I found this thread worth reading:
>
> https://list.nih.gov/cgi-bin/wa?A2=ind0705&L=IMAGEJ&P=R7156&I=-3
>
> which includes a macro for the nearest neighbour graph (using the centre of
> mass of particles).
>
> https://list.nih.gov/cgi-bin/wa?A2=ind0705&L=IMAGEJ&D=0&I=-3&P=14790
>
> Cheers
>
> G.

[BenTupper]

Hi,

On Mar 7, 2010, at 12:58 PM, Maria Rubio wrote:

> Thanks f ro your discussion.
>
> I'm interested on detecting a change in the distribution of gold  
> particles between control and experimental. My images come from SDS-
> FRL replica immunolabeling of synapses.
> so I think getting the distance between/among the particles I could  
> get the numerical data for later on doing some statistics!!
>

I just posted a plugin that computes the distance between object  
boundaries.  I wonder if it will provide you with what you are looking  
for.

http://imagejdocu.tudor.lu/doku.php?id=plugin:analysis:minimum_separation_distance:start

Ben

> Best!
>
> Maria
>
>
> Maria E. Rubio M.D./Ph.D
> Department of Otolaryngology
> University of Pittsburgh Medical School
> BST3 Building
> 3501 Fifth Avenue #10015
> Pittsburgh, PA 15261
> Phone: [phone]
> Fax: [phone]
> e-mail: [hidden email]
>
> On Mar 7, 2010, at 5:39 AM, Gabriel Landini wrote:
>
>> On Sunday 07 March 2010, you wrote:
>>> ... interesting thread!
>>
>> And after a feeling of deja-vu I found this thread worth reading:
>>
>> https://list.nih.gov/cgi-bin/wa?A2=ind0705&L=IMAGEJ&P=R7156&I=-3
>>
>> which includes a macro for the nearest neighbour graph (using the  
>> centre of
>> mass of particles).
>>
>> https://list.nih.gov/cgi-bin/wa?A2=ind0705&L=IMAGEJ&D=0&I=-3&P=14790
>>
>> Cheers
>>
>> G.

[Gabriel Landini]

Related to this thread, I by chance I saw this today:

Journal of Microscopy: Quantitative analysis and modelling of hepatic iron
stores using stereology and spatial statistics (p )
N.R. GHUGRE, I. GONZALEZ-GOMEZ, H. SHIMADA, T.D. COATES, J.C. WOOD

http://www3.interscience.wiley.com/cgi-bin/fulltext/123233954/PDFSTART

Cheers,

G