http://imagej.273.s1.nabble.com/Pair-correlation-function-on-ImageJ-tp5013569p5013725.html
Ph.D. Candidate in Chemistry
> Hi Xaio and Herbie,
>
> Apologies that this is straying in its relevance from the ImageJ list.
> Please email me off list if I can help further.
>
> But for completeness here is a method to get the g(r) for the pairwise
> correlation function (images attached). You might need to consider cropping
> the image depending on what you are interested in.
>
> Herbie I'd be interested to know if something similar can be generated
> using standard ImageJ methods.
>
> Using R and ImageJ in a workflow like this can be very useful especially
> when complex summary statistics are needed.
>
> Best wishes
> Richard
>
> In ImageJ:
>
> ///////////////////////////////////
> //something like this gives you the positions
> run("8-bit");
> setThreshold(148, 255);
> run("Analyze Particles...", "size=2-Infinity display exclude clear add
> in_situ");
> selectWindow("Results");
> saveAs("Results", "/your_dir/PPP.csv");
>
> //end
>
> Then in R with the package spatstat installed:
>
> ###################
> library(spatstat)
> setwd("/your_dir/")
> data1 = read.csv("PPP.csv")
> attach(data1)
> x <- data1[[03]]
> y <- data1[[04]]
> plot(x,y)#to check the data is the data looks OK
> data2 <- ppp(x, y, xrange=c(0,464), yrange=c(0,377))#note dimensions of
> your image
> pcf1 = pcf(data2)
> plot(pcf1)
>
> #end
>
>
>
>
> On 15/07/15 20:05, Xiao Zhong wrote:
>
>> 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>>>>>>
>>>>>>
>>>>>> --
>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>>>
>>>>>
>>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>>
>>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
>
> --
> Dr Richard Mort
> Research Fellow
> MRC Human Genetics Unit
> Institute of Genetics and Molecular Medicine
> University of Edinburgh
> Western General Hospital
> Crewe Road
> Edinburgh
> EH4 2XU
>
> Tel: 0131 651 8648
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
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