Extracting individual .tiffs from large number of ROIs

[Nickwheeler]

Relatively new to ImageJ so please bear with me.

I am trying to 'fragment' a larger image into lots of smaller ones, which I
can then analyse individually. To do this I create a Voronoi pattern,
overlay it onto my image of interest and invert the selection. This creates
anything from 2 to 2000 smaller ROIs, which I add to the ROI manager. This
adds the entire set of ROIs as one large selection, which I can then split
up into the individual ROIs and save as an ROIset.zip. I checked the ROIs by
labelling them and they are correctly selected, but after this I get stuck.

Ideally I would like to save each ROI as an individual .tiff file so I can
batch process them, how can I do this? Alternatively, if this is not
possible, can I get a colour histogram for each of these particles without
extracting them into separate files?

The goal is to simulate a fragmentation process and determine the chemical
make-up of the 'daughter particles'. I have a single RGB image (no slices)
from a scanning electron microscope, where different colours represent
different phases. So my goal is to extract the colour data from each
individual ROI image and export it into a central Excel file. The colour
data represents abundance of particular chemical phases which I can then use
for further analysis.

Thanks in advance for your help!!!
Nick



PS This thread got closest to my question but I got lost after exporting the
data to ROIset.zip, and I'm not working with stacks
http://imagej.1557.x6.nabble.com/I-need-to-copy-and-crop-mutiple-ROI-from-each-image-td5000475.html

[Rasband, Wayne (NIH/NIMH) [E]]

On Feb 21, 2014, at 12:18 PM, Nickwheeler wrote:

> Relatively new to ImageJ so please bear with me.
>
> I am trying to 'fragment' a larger image into lots of smaller ones, which I
> can then analyse individually. To do this I create a Voronoi pattern,
> overlay it onto my image of interest and invert the selection. This creates
> anything from 2 to 2000 smaller ROIs, which I add to the ROI manager. This
> adds the entire set of ROIs as one large selection, which I can then split
> up into the individual ROIs and save as an ROIset.zip. I checked the ROIs by
> labelling them and they are correctly selected, but after this I get stuck.
>
> Ideally I would like to save each ROI as an individual .tiff file so I can
> batch process them, how can I do this? Alternatively, if this is not
> possible, can I get a colour histogram for each of these particles without
> extracting them into separate files?

You can get the color histograms of each of the particles without extracting them into separate files. With n ROIs in the ROI Manager, the following JavaScript creates a table with n*3 rows and 256 columns (see screenshot). For each ROI, there are three rows in the table labeled Ri, Gi and Bi that contain the 256 red, green and blue histogram counts for the ROI with index 'i'.

-wayne

  imp = IJ.getImage();
  ip = imp.getProcessor();
  rm = RoiManager.getInstance();
  rois = rm.getRoisAsArray();
  rt = new ResultsTable();
  for (i=0; i<rois.length; i++) {
     ip.setRoi(rois[i]);
     ip.setRGBWeights(1, 0, 0);
     histogram = ip.getHistogram();
     rt.incrementCounter();
     rt.addValue("ROI", "R"+i);
     for (j=0; j<256; j++)
        rt.addValue("C"+j, histogram[j]);
     ip.setRGBWeights(0, 1, 0);
     histogram = ip.getHistogram();
     rt.incrementCounter();
     rt.addValue("ROI", "G"+i);
     for (j=0; j<256; j++)
        rt.addValue("C"+j, histogram[j]);
     ip.setRGBWeights(0, 0, 1);
     histogram = ip.getHistogram();
     rt.incrementCounter();
     rt.addValue("ROI", "B"+i);
     for (j=0; j<256; j++)
        rt.addValue("C"+j, histogram[j]);
  }
  rt.showRowNumbers(false);
  rt.show("Results");

[cid:[hidden email]]

>
> The goal is to simulate a fragmentation process and determine the chemical
> make-up of the 'daughter particles'. I have a single RGB image (no slices)
> from a scanning electron microscope, where different colours represent
> different phases. So my goal is to extract the colour data from each
> individual ROI image and export it into a central Excel file. The colour
> data represents abundance of particular chemical phases which I can then use
> for further analysis.
>
> Thanks in advance for your help!!!
> Nick
>
>
>
> PS This thread got closest to my question but I got lost after exporting the
> data to ROIset.zip, and I'm not working with stacks
> http://imagej.1557.x6.nabble.com/I-need-to-copy-and-crop-mutiple-ROI-from-each-image-td5000475.html
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Extracting-individual-tiffs-from-large-number-of-ROIs-tp5006620.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Nickwheeler]

Thanks Wayne! That looks like it'll give me the data I need.

Never done any Java programming before, how do I implement this javascript? I tried to put it into a plugin, but get 56 errors saying 'Cannot find symbol' when I compile and run.

This is the code I tried:

import ij.*;
import ij.process.*;
import ij.gui.*;
import java.awt.*;
import ij.plugin.*;
import ij.plugin.frame.*;

public class MultiROIhist_ implements PlugIn {

        public void run(String arg) {
                ImagePlus imp = IJ.getImage();
                IJ.run(imp, "Invert", "");
                IJ.wait(1000);
                IJ.run(imp, "Invert", "");
        }

imp = IJ.getImage();
  ip = imp.getProcessor();
  rm = RoiManager.getInstance();
  rois = rm.getRoisAsArray();
  rt = new ResultsTable();
  for (i=0; i<rois.length; i++) {
     ip.setRoi(rois[i]);
     ip.setRGBWeights(1, 0, 0);
     histogram = ip.getHistogram();
     rt.incrementCounter();
     rt.addValue("ROI", "R"+i);
     for (j=0; j<256; j++)
        rt.addValue("C"+j, histogram[j]);
     ip.setRGBWeights(0, 1, 0);
     histogram = ip.getHistogram();
     rt.incrementCounter();
     rt.addValue("ROI", "G"+i);
     for (j=0; j<256; j++)
        rt.addValue("C"+j, histogram[j]);
     ip.setRGBWeights(0, 0, 1);
     histogram = ip.getHistogram();
     rt.incrementCounter();
     rt.addValue("ROI", "B"+i);
     for (j=0; j<256; j++)
        rt.addValue("C"+j, histogram[j]);
  }
  rt.showRowNumbers(false);
  rt.show("Results");

}

[Rasband, Wayne (NIH/NIMH) [E]]

On Feb 22, 2014, at 10:29 AM, Nickwheeler wrote:

> Thanks Wayne! That looks like it'll give me the data I need.
>
> Never done any Java programming before, how do I implement this javascript?

JavaScript and Java are not the same thing. JavaScript is an easier to use scripting language. To run this JavaScript, open a new editor window (Plugins>New>JavaScript), paste the script into the window and type ctrl+j (Macros>Evaluate JavaScript).

-wayne

> I tried to put it into a plugin, but get 56 errors saying 'Cannot find
> symbol' when I compile and run.
>
> This is the code I tried:
>
> import ij.*;
> import ij.process.*;
> import ij.gui.*;
> import java.awt.*;
> import ij.plugin.*;
> import ij.plugin.frame.*;
>
> public class MultiROIhist_ implements PlugIn {
>
> public void run(String arg) {
> ImagePlus imp = IJ.getImage();
> IJ.run(imp, "Invert", "");
> IJ.wait(1000);
> IJ.run(imp, "Invert", "");
> }
>
> imp = IJ.getImage();
>  ip = imp.getProcessor();
>  rm = RoiManager.getInstance();
>  rois = rm.getRoisAsArray();
>  rt = new ResultsTable();
>  for (i=0; i<rois.length; i++) {
>     ip.setRoi(rois[i]);
>     ip.setRGBWeights(1, 0, 0);
>     histogram = ip.getHistogram();
>     rt.incrementCounter();
>     rt.addValue("ROI", "R"+i);
>     for (j=0; j<256; j++)
>        rt.addValue("C"+j, histogram[j]);
>     ip.setRGBWeights(0, 1, 0);
>     histogram = ip.getHistogram();
>     rt.incrementCounter();
>     rt.addValue("ROI", "G"+i);
>     for (j=0; j<256; j++)
>        rt.addValue("C"+j, histogram[j]);
>     ip.setRGBWeights(0, 0, 1);
>     histogram = ip.getHistogram();
>     rt.incrementCounter();
>     rt.addValue("ROI", "B"+i);
>     for (j=0; j<256; j++)
>        rt.addValue("C"+j, histogram[j]);
>  }
>  rt.showRowNumbers(false);
>  rt.show("Results");
>
> }
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Extracting-individual-tiffs-from-large-number-of-ROIs-tp5006620p5006631.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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