Pair correlation function on ImageJ
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Pair correlation function on ImageJ
 
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Re: Pair correlation function on ImageJ
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Re: Pair correlation function on ImageJ
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Re: Pair correlation function on ImageJ
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Re: Pair correlation function on ImageJ
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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 |
Colloidal Packing.png (252K)
Re: Pair correlation function on ImageJ
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Re: Pair correlation function on ImageJ
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In reply to this post by Xiao Zhong
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. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Pair correlation function on ImageJ
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