Re: Pair correlation function on ImageJ

Posted by Xiao Zhong on
URL: http://imagej.273.s1.nabble.com/Pair-correlation-function-on-ImageJ-tp5013569p5013579.html

Hi everyone,

Thanks for the reply. I have attached a piece of my data here. I just
wanted to calculate the pair correlation function of these particles
(g(r)). Since I know different packings would give different g(r).  This
attached image has spheres roughly form a 2D close packing, which should
give a g(r) that is different than other types of packings.

I'd appreciate any inputs on this issue.

Thanks,
Xiao

Xiao Zhong
Ph.D. Candidate in Chemistry
Department of Chemistry and Molecular Design Institute
New York University

On Wed, Jul 15, 2015 at 11:58 AM, Herbie <[hidden email]> wrote:

> Dear Richard,
>
> the poster Xiao is not very clear, or at least I don't know what "packed
> particles" are.
>
> If "pair correlation function of a certain 2D area" means pixel-pair
> correlation in that area, I'm pretty sure that this spatial statistic is
> identical to the auto-correlation function of the image in this area.
>
> Best
>
> Herbie
>
> ::::::::::::::::::::::::::::::::::::::::::
> Am 15.07.15 um 17:38 schrieb Richard Mort:
>
>  I think in this context Xiao is looking for the spatial statistic. I'm
>> not aware of an IJ plugin to do this at the moment but it is on my to do
>> list as its a very useful method. The quickest approach would be to
>> segment your images and then use analyze particles to get the XY
>> positions of each object. Save as .csv and then import this data into R
>> and use the spatstat package:
>>
>> http://www.inside-r.org/packages/cran/spatstat/docs/pcf
>>
>> Best
>> R
>>
>> On 15/07/15 16:16, Herbie wrote:
>>
>>> Xiao,
>>>
>>> it's always a good idea to first consult the user guide...
>>>
>>> You may have a look at page
>>>
>>> <http://rsb.info.nih.gov/ij/docs/guide/146-29.html#toc-Subsection-29.10>
>>>
>>> Subsection " 29.10.7 FD Math… "
>>>
>>> If you use Image1 = Image2, i.e. the same image, then you get the
>>> auto-correlation function and I guess this is what you want.
>>>
>>> HTH
>>>
>>> Herbie
>>>
>>> ::::::::::::::::::::::::::::::::::::::::
>>> Am 15.07.15 um 15:29 schrieb Xiao Zhong:
>>>
>>>> Hi everyone,
>>>>
>>>> I am Ph.D. candidate and am working on a project concerning colloidal
>>>> particle packing. I am new to ImageJ and I was wondering if anyone knows
>>>> how to use it to calculate pair correlation function of a certain 2D
>>>> area
>>>> with packed particles.
>>>>
>>>> Thanks!
>>>>
>>>> Best,
>>>> Xiao
>>>>
>>>> --
>>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>>
>>>>
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>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
>>
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