Radial profile ext to work with Macros
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Dear Philippe, Thanks again for your help and patience. The macro you posted is exactly what i was after.
can be found under the following link: have some doubts or misunderstanding? This is a great addition. What defines the size and number of the radii My question here was about what defines the incremental increase in radius from the centre. ie if the radius is set to 6.0 pixels 4 results are returned at a radius of 1.5, 3, 4.5, 6.
Thanks again JAmes
Dr James Burchfield The Garvan Institute of Medical Research 384 Victoria Street Darlinghurst, NSW, 2010 Australia Email: [hidden email]
Phone:+61 2 92958229 Web: www.garvan.org.au On Thu, Feb 13, 2014 at 12:07 AM, Philippe CARL [via ImageJ] <[hidden email]> wrote: Dear James |
Re: Radial profile ext to work with Macros
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Dear James,
The "incremental increase in radius from the centre" is actually part of the native radial profile plugin (i.e. I haven't written this code). Nevertheless here is how it is calculated: for (i = 0; i < nBins; i++) dataX[i] = (float) (cal.pixelWidth * mR * ((double)(i + 1) / nBins)); with: mR the radius nBins = (int) (3*mR/4); cal.pixelWidth is the set calibration parameter in the case you activate the "Use Spatial Calibration" option and is equal to 1 otherwise Best regards, Philippe Philippe CARL Laboratoire de Biophotonique et Pharmacologie UMR 7213 CNRS - Université de Strasbourg Faculté de Pharmacie 74 route du Rhin 67401 ILLKIRCH Tel : +33(0)3 68 85 41 84 -----Message d'origine----- De : ImageJ Interest Group [mailto:[hidden email]] De la part de JimmiB Envoyé : jeudi 13 février 2014 00:37 À : [hidden email] Objet : Re: Radial profile ext to work with Macros Dear Philippe, Thanks again for your help and patience. The macro you posted is exactly what i was after. *I have added an "Application" tab at the bottom of the plugin Website > that * > > > *can be found under the following > link: http://punias.free.fr/radial-profile-ext.html > <http://punias.free.fr/radial-profile-ext.html>is this new addition > answering clearly your questions now or do you still * *have some doubts or misunderstanding? * This is a great addition. *What defines the size and number of the radii * My question here was about what defines the incremental increase in radius from the centre. ie if the radius is set to 6.0 pixels 4 results are returned at a radius of 1.5, 3, 4.5, 6. Thanks again JAmes *Dr James Burchfield* The Garvan Institute of Medical Research 384 Victoria Street Darlinghurst, NSW, 2010 Australia Email: [hidden email] Phone:+61 2 92958229 Web: *www.garvan.org.au <http://www.garvan.org.au>* On Thu, Feb 13, 2014 at 12:07 AM, Philippe CARL [via ImageJ] < [hidden email]> wrote: > Dear James > > > When I run this I get a results list with Time = Slice# and The > intensity > of the first radius. > > This looks good. > > Ok good... > > > How do i get this to plot, or add the other radius. > > Getting the data in a result table or plot is not very different in > terms of use of the "Ext." methods ; nevertheless, the following macro > will do the job you are looking for: > > for(rad = 200; rad <= 210; rad += 10) > raduisPlot(rad); > > function raduisPlot(radius) > { > selectWindow("confocal-series.tif"); > run("Radial Profile Angle", "x_center=200 y_center=200 > radius=" + radius + " starting_angle=0 integration_angle=180 > use_spatial_calibration calculate_radial_profile_on_stack"); > color = newArray("black", "blue", "cyan", "darkGray", "gray", > "green", "lightGray", "magenta", "orange", "pink", "red", "yellow"); > xValues = newArray(Ext.getStackSize); > yValues = newArray(Ext.getStackSize); > Plot.create("Radius = " + radius, "Time", "Fluorescence > (A.U.)", xValues, yValues); > Plot.setLimits(0, Ext.getStackSize, 0, 150); > for(j = 0; j != Ext.getBinSize; j++) > { > for(i = 0; i != Ext.getStackSize; i++) > { > xValues[i] = i; > yValues[i] = Ext.getYValue(i, j); > } > Plot.add("line", xValues, yValues); > Plot.setColor(color[j % 12]); > } > Plot.show(); > } > > > I was also wondering if you could clarify exactly what the starting > angle > (*seems pretty self explanatory)* and integration angle - (*Does this > define the number of sections the measurements are broken down into? > > each half of the ROI is analysed and then averaged to give the final > result?)* are. > > I have added an "Application" tab at the bottom of the plugin Website > that can be found under the following link: > http://punias.free.fr/radial-profile-ext.html > is this new addition answering clearly your questions now or do you > still have some doubts or misunderstanding? > > > Also, What defines the size and number of the radii Cheers, James > > I'm afraid that I don't understand this question. > Do you want to know what the values of "Ext.getStackSize" and > "Ext.getBinSize" are or something else? > > Best regards, > > Philippe > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > ------------------------------ > If you reply to this email, your message will be added to the > discussion > below: > > http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-work-with-Macro > s-tp5005598p5006503.html To unsubscribe from Radial profile ext to > work with Macros, click > here<http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=u > nsubscribe_by_code&node=5005598&code=ai5idXJjaGZpZWxkQGdhcnZhbi5vcmcuY > XV8NTAwNTU5OHw4Nzg1MTgwMTc=> > . > NAML<http://imagej.1557.x6.nabble.com/template/NamlServlet.jtp?macro=m > acro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.nam > espaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble > .view.web.template.NodeNamespace&breadcrumbs=notify_subscribers%21nabb > le%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_emai > l%21nabble%3Aemail.naml> > -- View this message in context: http://imagej.1557.x6.nabble.com/Radial-profile-ext-to-work-with-Macros-tp50 05598p5006508.html Sent from the ImageJ mailing list archive at Nabble.com. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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