Center of mass for a channel

[Juanjo Vega]

Hello,

I'm developing a plugin and I need to calculate the center of mass for an image's red channel (I allow to select the channel from a combobox for convenience, but it's intended to work mainly with the red one)

My images contain cells and some of them are pretty close to others, so I need to work with a ROI.

The thing is to extract the channel, set the ROI (which comes from the main image) and get the center of mass point with getStatistics().

My method to get the Center of Mass for a concrete channel is the following, but it doesn't seem to work, as the point appears outside of the ROI.

Any tip? Or does anybody know if there is a better way to do this?


    private Point getCenterOfMass(ImagePlus imp, int channel) {
        RGBStackSplitter splitter = new RGBStackSplitter();
        splitter.split(imp.getStack(), true);

        ImageStack stack = null;
        switch (channel) {
            case 0:
                stack = splitter.red;
                break;
            case 1:
                stack = splitter.green;
                break;
            case 2:
                stack = splitter.blue;
        }

        ImagePlus aux = new ImagePlus("CM", stack.getProcessor(1));
        aux.copyScale(imp);
        aux.setCalibration(imp.getCalibration());
        aux.setRoi(imp.getRoi());

        ImageStatistics is = aux.getStatistics(ImageStatistics.CENTER_OF_MASS);

        Point CM = new Point();
        CM.setLocation(is.xCenterOfMass, is.yCenterOfMass);

        return CM;
    }


Sincerely,


------------------------------------------------------------
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.csic.es

[phone]

"Las mejores almas son capaces de los mayores vicios como de las mayores
virtudes, y aquellos que caminan despacio por el camino recto pueden
llegar más lejos que los que corren pero se apartan de él." - Discurso
del Método, René Descartes.

[Peter Haub]

Hi,

I've checked your code and can not see any problem (with an simple image
example).

Are you sure that the CM has to be inside the ROI?
It's not a must.

ph


On 19.07.2011 18:06, Juanjo Vega wrote:

> Hello,
>
> I'm developing a plugin and I need to calculate the center of mass for an image's red channel (I allow to select the channel from a combobox for convenience, but it's intended to work mainly with the red one)
>
> My images contain cells and some of them are pretty close to others, so I need to work with a ROI.
>
> The thing is to extract the channel, set the ROI (which comes from the main image) and get the center of mass point with getStatistics().
>
> My method to get the Center of Mass for a concrete channel is the following, but it doesn't seem to work, as the point appears outside of the ROI.
>
> Any tip? Or does anybody know if there is a better way to do this?
>
>
>      private Point getCenterOfMass(ImagePlus imp, int channel) {
>          RGBStackSplitter splitter = new RGBStackSplitter();
>          splitter.split(imp.getStack(), true);
>
>          ImageStack stack = null;
>          switch (channel) {
>              case 0:
>                  stack = splitter.red;
>                  break;
>              case 1:
>                  stack = splitter.green;
>                  break;
>              case 2:
>                  stack = splitter.blue;
>          }
>
>          ImagePlus aux = new ImagePlus("CM", stack.getProcessor(1));
>          aux.copyScale(imp);
>          aux.setCalibration(imp.getCalibration());
>          aux.setRoi(imp.getRoi());
>
>          ImageStatistics is = aux.getStatistics(ImageStatistics.CENTER_OF_MASS);
>
>          Point CM = new Point();
>          CM.setLocation(is.xCenterOfMass, is.yCenterOfMass);
>
>          return CM;
>      }
>
>
> Sincerely,
>
>
> ------------------------------------------------------------
> Juanjo Vega ([hidden email])
>
> Unidad de Biocomputación. Laboratorio B-13.
> Centro Nacional de Biotecnología. CNB-CSIC.
> C\ Darwin, 3. Campus de Cantoblanco.
> Universidad Autónoma de Madrid.
> 28049, Madrid, Spain.
>
> http://www.cnb.csic.es
> http://www.biocomp.cnb.csic.es
>
> [phone]
>
> "Las mejores almas son capaces de los mayores vicios como de las mayores
> virtudes, y aquellos que caminan despacio por el camino recto pueden
> llegar más lejos que los que corren pero se apartan de él." - Discurso
> del Método, René Descartes.
>

[Juanjo Vega]

Hi,

Yesterday I managed to fix the problem.

The point was calculated properly, but when drawing it into the image, it was in a wrong position.

If I copy scale and calibration after obtaining the center of mass it works fine.

>  aux.copyScale(imp);
>  aux.setCalibration(imp.getCalibration());


I still don't understand why, but now it's working :)

Thank you very much for your help :)

Sincerely,

Juanjo


On Jul 21, 2011, at 10:51 AM, Peter Haub wrote:

> Hi,
>
> I've checked your code and can not see any problem (with an simple image example).
>
> Are you sure that the CM has to be inside the ROI?
> It's not a must.
>
> ph
>
>
> On 19.07.2011 18:06, Juanjo Vega wrote:
>> Hello,
>>
>> I'm developing a plugin and I need to calculate the center of mass for an image's red channel (I allow to select the channel from a combobox for convenience, but it's intended to work mainly with the red one)
>>
>> My images contain cells and some of them are pretty close to others, so I need to work with a ROI.
>>
>> The thing is to extract the channel, set the ROI (which comes from the main image) and get the center of mass point with getStatistics().
>>
>> My method to get the Center of Mass for a concrete channel is the following, but it doesn't seem to work, as the point appears outside of the ROI.
>>
>> Any tip? Or does anybody know if there is a better way to do this?
>>
>>
>>     private Point getCenterOfMass(ImagePlus imp, int channel) {
>>         RGBStackSplitter splitter = new RGBStackSplitter();
>>         splitter.split(imp.getStack(), true);
>>
>>         ImageStack stack = null;
>>         switch (channel) {
>>             case 0:
>>                 stack = splitter.red;
>>                 break;
>>             case 1:
>>                 stack = splitter.green;
>>                 break;
>>             case 2:
>>                 stack = splitter.blue;
>>         }
>>
>>         ImagePlus aux = new ImagePlus("CM", stack.getProcessor(1));
>>         aux.copyScale(imp);
>>         aux.setCalibration(imp.getCalibration());
>>         aux.setRoi(imp.getRoi());
>>
>>         ImageStatistics is = aux.getStatistics(ImageStatistics.CENTER_OF_MASS);
>>
>>         Point CM = new Point();
>>         CM.setLocation(is.xCenterOfMass, is.yCenterOfMass);
>>
>>         return CM;
>>     }
>>
>>
>> Sincerely,
>>
>>
>> ------------------------------------------------------------
>> Juanjo Vega ([hidden email])
>>
>> Unidad de Biocomputación. Laboratorio B-13.
>> Centro Nacional de Biotecnología. CNB-CSIC.
>> C\ Darwin, 3. Campus de Cantoblanco.
>> Universidad Autónoma de Madrid.
>> 28049, Madrid, Spain.
>>
>> http://www.cnb.csic.es
>> http://www.biocomp.cnb.csic.es
>>
>> [phone]
>>
>> "Las mejores almas son capaces de los mayores vicios como de las mayores
>> virtudes, y aquellos que caminan despacio por el camino recto pueden
>> llegar más lejos que los que corren pero se apartan de él." - Discurso
>> del Método, René Descartes.
>>

------------------------------------------------------------
Juanjo Vega ([hidden email])

Unidad de Biocomputación. Laboratorio B-13.
Centro Nacional de Biotecnología. CNB-CSIC.
C\ Darwin, 3. Campus de Cantoblanco.
Universidad Autónoma de Madrid.
28049, Madrid, Spain.

http://www.cnb.csic.es
http://www.biocomp.cnb.csic.es

[phone]

"Las mejores almas son capaces de los mayores vicios como de las mayores
virtudes, y aquellos que caminan despacio por el camino recto pueden
llegar más lejos que los que corren pero se apartan de él." - Discurso
del Método, René Descartes.