Calculating the area of one channel within an 'island' of a another channel
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Calculating the area of one channel within an 'island' of a another channel
 
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Re: Calculating the area of one channel within an 'island' of a another channel
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Re: Calculating the area of one channel within an 'island' of a another channel
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Re: Calculating the area of one channel within an 'island' of a another channel
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Re: Calculating the area of one channel within an 'island' of a another channel
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No it still gets scrambled Here is the original file
2013/7/3 Stoyan Pavlov <[hidden email]>: > Hi Angus, > The email converted the long lines into several rows so the correct > macro is this one: > // This Macro counts particles inside specific Roi and otputs the > number to TAB separated Log window which after saving can be imported > to excel. > print ("RoiNumber"," ","SliceLabel"," ","RoIName"," > ","Count"," ","RoIArea"," ","RoIPerimeter"," "," > ParticlesCoveredArea"," ","AreaFraction") ; > setAutoThreshold("Default dark"); > n = roiManager("count"); > for (i=0; i<n; i++) { > roiManager("select", i); > run("Set Measurements...", "area perimeter redirect=None decimal=4"); > run("Measure"); > r=getResult("Area"); > u=getResult("Perim."); > run("Set Measurements...", "area area_fraction limit display > redirect=None decimal=4"); > run("Measure"); > s=getResult("Area"); > t=getResult("%Area"); > run("Analyze Particles...", "size=0-infinity circularity=0.00-1.00 > show=Nothing display clear "); > m=nResults; > q=getInfo("slice.label"); > print (i," ",q," > ",call("ij.plugin.frame.RoiManager.getName", i)," ",m," ",r," > ",u," ",s," ",t) ; > } > If ity still gets converted to multiple lines, know that each line > between () should be on one row and there are TABs between the " " > which seem empty. > Stoyan > > 2013/7/3 Angus G <[hidden email]>: >> Hi Stoyan! >> >> Firstly thank you! How exactly do I get the macro to run? I tried going to >> plugin -> new -> macro then pasted in: >> >> >> print ("RoiNumber"," ","SliceLabel"," ","RoIName"," ","Count"," >> ","RoIArea"," ","RoIPerimeter"," "," ParticlesCoveredArea"," >> ","AreaFraction") ; >> setAutoThreshold("Default dark"); >> n = roiManager("count"); >> for (i=0; i<n; i++) { >> roiManager("select", i); >> run("Set Measurements...", "area perimeter redirect=None >> decimal=4"); >> run("Measure"); >> r=getResult("Area"); >> u=getResult("Perim."); >> run("Set Measurements...", "area area_fraction limit display redirect=None >> decimal=4"); >> run("Measure"); >> s=getResult("Area"); >> t=getResult("%Area"); >> run("Analyze Particles...", "size=0-infinity circularity=0.00-1.00 >> show=Nothing display clear "); >> m=nResults; >> q=getInfo("slice.label"); >> print (i," ",q," ",call("ij.plugin.frame.RoiManager.getName", >> i)," ",m," ",r," ",u," ",s," ",t) ; >> } >> >> But when I try to run it I get the message: >> >> ')' expected in line 2 >> <",">RolArea"," ","RolPerimeter"," ","ParticlesCoveredArea"," >> >> Is this the right way to try and run the macro or am I doing something >> grossly wrong? (I have never dealt with macros before!) >> >> Thanks again! >> Angus >> >> -----Original Message----- From: Stoyan Pavlov >> Sent: Wednesday, July 03, 2013 1:37 PM >> To: [hidden email] >> Subject: Re: Calculating the area of one channel within an 'island' of a >> another channel >> >> Hi Angus, >> *You may try adding the "Islands*" as RoIs to the RoIManager (simply by >> >> running the particle analyzer with the add to manager option on) and than >> using a simple macro you may measure anything within each of the RoIs. I >> used to do something similar with the following macro: >> >> / This Macro counts particles inside specific Roi and otputs the number to >> TAB separated Log window which after saving can be imported to excel. >> print ("RoiNumber"," ","SliceLabel"," ","RoIName"," ","Count"," >> ","RoIArea"," ","RoIPerimeter"," "," ParticlesCoveredArea"," >> ","AreaFraction") ; >> setAutoThreshold("Default dark"); >> n = roiManager("count"); >> for (i=0; i<n; i++) { >> roiManager("select", i); >> run("Set Measurements...", "area perimeter redirect=None >> decimal=4"); >> run("Measure"); >> r=getResult("Area"); >> u=getResult("Perim."); >> run("Set Measurements...", "area area_fraction limit display redirect=None >> decimal=4"); >> run("Measure"); >> s=getResult("Area"); >> t=getResult("%Area"); >> run("Analyze Particles...", "size=0-infinity circularity=0.00-1.00 >> show=Nothing display clear "); >> m=nResults; >> q=getInfo("slice.label"); >> print (i," ",q," ",call("ij.plugin.frame.RoiManager.getName", >> i)," ",m," ",r," ",u," ",s," ",t) ; >> } >> >> I hope this helps. >> >> Stoyan >> >> >> 2013/7/3 Angus G <[hidden email]> >> >>> Dear all, >>> >>> Even if people don’t have a mechanism to achieve this it would be good to >>> know if it is possible. >>> >>> I invert my images, split them into three channels (RBG) and then >>> threshold them. I then use watershed to break up the red channel data into >>> ‘islands’ of particles. When I use ‘analyse particles’ each ‘island’ gets >>> it’s own number and I can obtain the area in pixels of each of these. >>> All’s >>> good so far! >>> >>> What I would like to be able to do is quantify the area of yellow pixels >>> within each numbered ‘island’ of red pixels. >>> >>> If anyone has any ideas or knows if this will not be possible I’d be >>> really grateful if you could let me know. If it can be done it will change >>> the way I gather data and would greatly improve the results! >>> >>> Thanks for any help you can provide! >>> abg >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >>> >> >> >> >> -- >> Dr. Stoyan P. Pavlov, MD, PhD >> Departament of Anatomy, Histology and Embryology >> Medical University "Prof. Dr. Paraskev Stoyanov", Varna >> Prof. Marin Drinov Str.55 >> 9002 Varna >> Bulgaria >> Tel: +359 (0) 52 - 677 - 052 >> e-mail: [hidden email] >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > Dr. Stoyan P. Pavlov, MD, PhD > Departament of Anatomy, Histology and Embryology > Medical University "Prof. Dr. Paraskev Stoyanov", Varna > Prof. Marin Drinov Str.55 > 9002 Varna > Bulgaria > Tel: +359 (0) 52 - 677 - 052 > e-mail: [hidden email] -- Dr. Stoyan P. Pavlov, MD, PhD Departament of Anatomy, Histology and Embryology Medical University "Prof. Dr. Paraskev Stoyanov", Varna Prof. Marin Drinov Str.55 9002 Varna Bulgaria Tel: +359 (0) 52 - 677 - 052 e-mail: [hidden email] -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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