I am working on a plugin to create image slices to form a image stack based
on a set of data points (x and y). Any tips? :) |
On a similar lines..I am keen too I have data with X, Y and Z (stacks). Is
it possible to have 3 D projection from x, y, z? Best, Yaseen On 7 March 2012 17:54, Melissa Goh <[hidden email]> wrote: > I am working on a plugin to create image slices to form a image stack based > on a set of data points (x and y). Any tips? :) > |
In reply to this post by Melissa Goh
Hi Wayne,
Yes the data points (x,y,z) are stored in a text file. The z will be the slice number and the x and y will be used to draw pixel for each slice. Best regards, Melissa On Thu, Mar 8, 2012 at 2:21 AM, Rasband, Wayne (NIH/NIMH) [E] < [hidden email]> wrote: > Hi Melissa, > > On Mar 7, 2012, at 12:54 PM, Melissa Goh wrote: > > > I am working on a plugin to create image slices to form a image stack > based > > on a set of data points (x and y). Any tips? :) > > I should be able to write a macro that does this, but I need a little more > information. Why do you need a stack if all you have are (x,y) data points? > Are the data points in a text file? > > Best regards, > > -wayne > > |
Hi,
You can also have a look to 3d tools on the wiki : http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_tools:start Thomas Le 07/03/2012 19:30, Melissa Goh a écrit : > Hi Wayne, > > Yes the data points (x,y,z) are stored in a text file. The z will be the > slice number and the x and y will be used to draw pixel for each slice. > > Best regards, > Melissa > > On Thu, Mar 8, 2012 at 2:21 AM, Rasband, Wayne (NIH/NIMH) [E]< > [hidden email]> wrote: > >> Hi Melissa, >> >> On Mar 7, 2012, at 12:54 PM, Melissa Goh wrote: >> >>> I am working on a plugin to create image slices to form a image stack >> based >>> on a set of data points (x and y). Any tips? :) >> I should be able to write a macro that does this, but I need a little more >> information. Why do you need a stack if all you have are (x,y) data points? >> Are the data points in a text file? >> >> Best regards, >> >> -wayne >> >> > -- /**********************************************************/ Thomas Boudier, MCU Université Pierre et Marie Curie, Modélisation Cellulaire et Imagerie Biologique (EE1), IFR 83, Bat B 7ème étage, porte 723, Campus Jussieu. Tel : 01 44 27 46 92 Fax : 01 44 27 22 91 /*******************************************************/ |
In reply to this post by Melissa Goh
On Mar 7, 2012, at 12:54 PM, Melissa Goh wrote:
> I am working on a plugin to create image slices to form a image stack based > on a set of data points (x and y). Any tips? :) Here is a plugin that plots a list of x,y,z values in a text file on a 512x512x512 stack. -wayne import ij.*; import ij.plugin.*; import ij.measure.ResultsTable; import ij.util.Tools; public class Plot_XYZ implements PlugIn { public void run(String arg) { int size = 512; // stack size ImagePlus imp = IJ.createImage("Untitled", "8-bit black", size, size, size); IJ.run("Results... "); // file>import>results ResultsTable rt = ResultsTable.getResultsTable(); if (rt==null) return; double[] x = rt.getColumnAsDoubles(0); double[] y = rt.getColumnAsDoubles(1); double[] z = rt.getColumnAsDoubles(2); double[] mm = Tools.getMinMax(x); double xmin=mm[0], xmax=mm[1]; mm = Tools.getMinMax(y); double ymin=mm[0], ymax=mm[1]; mm = Tools.getMinMax(z); double zmin=mm[0], zmax=mm[1]; ImageStack stack = imp.getStack(); int xc, yc, zc; for (int i=0; i<x.length; i++) { xc = (int)((x[i]-xmin)*size/(xmax-xmin)+0.5); yc = (int)((y[i]-ymin)*size/(ymax-ymin)+0.5); zc = (int)((z[i]-zmin)*size/(zmax-zmin)+0.5); stack.setVoxel(xc, yc, zc, 255); } imp.show(); } } |
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