Fwd: What simple should this be....

[Jonas Boehnke]

Hello guys!

For sure this is a simple task but I am trying and not getting it done.
I want some particles to be selected *by color**treshold*.
Please see the excample tiff file attached, it is just an excample to
illustrae the principle.
I want the large blue particles (including the green inclusions) on the
right selected without having the blue on the left side selected...

But how?

Best regards,
Jonas


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

[Sidnei Paciornik]

I guess there are several solutions. Here is one, considering you only want
blue particles that contain green ones.

Color threshold to select green regions. Dilate result.
Color threshold to select blue regions.
Use a function to mark the blue objects that touch the dilated green
objects. This function is available in tbe Biovoxxel set of plugins (
http://www.biovoxxel.de/macros.html) by Jan Brocher.

Hope that helps.

Prof. Sidnei Paciornik
Grupo de Análise de Imagens e Microscopia Digital
DEMa <http://www.dema.puc-rio.br/> - Departamento de Engenharia de Materiais
PUC-Rio <http://www.puc-rio.br/>
Rua Marquês de São Vicente 225
Prédio Leme, Sala 501L
Gávea - Rio de Janeiro - RJ
22451-900 - Brasil
tel: [phone]





On Wed, Jun 12, 2013 at 7:07 AM, Jonas Boehnke <[hidden email]> wrote:

>
> Hello guys!
>
> For sure this is a simple task but I am trying and not getting it done.
> I want some particles to be selected *by color**treshold*.
> Please see the excample tiff file attached, it is just an excample to
> illustrae the principle.
> I want the large blue particles (including the green inclusions) on the
> right selected without having the blue on the left side selected...
>
> But how?
>
> Best regards,
> Jonas
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.**html<http://imagej.nih.gov/ij/list.html>
>

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

[Rob van 't Hof-2]

Hi,
It is fairly straightforward.  Macro at the end of this email.
I combined 2 colour thresholds, 1 to find blue objects, and one to find
green ones, Then I dilated the green objects and used the dilated image
as a seed in an binary reconstruct operation to find blue objects in
contact with the green ones. The binary reconstruct plugin is from
Gabriel Landini's Morpholoy collection of plugins, available from his
web site here:
http://www.dentistry.bham.ac.uk/landinig/software/software.html

The colour threshold code is generated by the colour threshold dialog by
hitting the "Macro" button (you do need to have the macro recorder
running to record this).

Hope this helps,

Rob

Macro:


run("Duplicate...", "title=in1");
run("Duplicate...", "title=in2");
selectWindow("in1");
//First select all blue particles
// Color Thresholder 1.47t
// Autogenerated macro, single images only!
min=newArray(3);
max=newArray(3);
filter=newArray(3);
a=getTitle();
run("HSB Stack");
run("Convert Stack to Images");
selectWindow("Hue");
rename("0");
selectWindow("Saturation");
rename("1");
selectWindow("Brightness");
rename("2");
min[0]=157;
max[0]=184;
filter[0]="pass";
min[1]=47;
max[1]=255;
filter[1]="pass";
min[2]=134;
max[2]=255;
filter[2]="pass";
for (i=0;i<3;i++){
   selectWindow(""+i);
   setThreshold(min[i], max[i]);
   run("Convert to Mask");
   if (filter[i]=="stop")  run("Invert");
}
imageCalculator("AND create", "0","1");
imageCalculator("AND create", "Result of 0","2");
for (i=0;i<3;i++){
   selectWindow(""+i);
   close();
}
selectWindow("Result of 0");
close();
selectWindow("Result of Result of 0");
rename(a);
// Colour Thresholding end of autogenerated code-------------

selectWindow("in2");
//Next select green particles
// Color Thresholder 1.47t
// Autogenerated macro, single images only!
min=newArray(3);
max=newArray(3);
filter=newArray(3);
a=getTitle();
run("HSB Stack");
run("Convert Stack to Images");
selectWindow("Hue");
rename("0");
selectWindow("Saturation");
rename("1");
selectWindow("Brightness");
rename("2");
min[0]=65;
max[0]=116;
filter[0]="pass";
min[1]=101;
max[1]=255;
filter[1]="pass";
min[2]=135;
max[2]=255;
filter[2]="pass";
for (i=0;i<3;i++){
   selectWindow(""+i);
   setThreshold(min[i], max[i]);
   run("Convert to Mask");
   if (filter[i]=="stop")  run("Invert");
}
imageCalculator("AND create", "0","1");
imageCalculator("AND create", "Result of 0","2");
for (i=0;i<3;i++){
   selectWindow(""+i);
   close();
}
selectWindow("Result of 0");
close();
selectWindow("Result of Result of 0");
rename(a);
// Colour Thresholding end of autogenerated code-------------

//now find blue objects with green centre
selectWindow("in2");
setOption("BlackBackground", true);
run("Dilate");
//use binary reconstruct from Gabriel Landini to find blue
//objects that overlap partially with green inner particles
run("BinaryReconstruct ", "mask=in1 seed=in2 create white");
rename("blue particles");
selectWindow("in2");
rename("green centers");
selectWindow("in1");
close();

On 12/06/2013 11:07, Jonas Boehnke wrote:

>
> Hello guys!
>
> For sure this is a simple task but I am trying and not getting it done.
> I want some particles to be selected *by color**treshold*.
> Please see the excample tiff file attached, it is just an excample to
> illustrae the principle.
> I want the large blue particles (including the green inclusions) on
> the right selected without having the blue on the left side selected...
>
> But how?
>
> Best regards,
> Jonas
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
_____________________________
Dr. Rob van 't Hof
Reader

Centre for Molecular Medicine
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom


Phone: [phone]
email: [hidden email]
_____________________________


The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

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

[Gabriel Landini]

On Wednesday 12 Jun 2013 13:06:37 Rob van 't Hof wrote:

> It is fairly straightforward.  Macro at the end of this email.
> I combined 2 colour thresholds, 1 to find blue objects, and one to find
> green ones, Then I dilated the green objects and used the dilated image
> as a seed in an binary reconstruct operation to find blue objects in
> contact with the green ones. The binary reconstruct plugin is from
> Gabriel Landini's Morpholoy collection of plugins, available from his
> web site here:
> http://www.dentistry.bham.ac.uk/landinig/software/software.html
>
> The colour threshold code is generated by the colour threshold dialog by
> hitting the "Macro" button (you do need to have the macro recorder
> running to record this).

That is a way of doing it, however it would fail if one blue regions touches
(but does not surround) a green region.

A way of avoiding this is to segment the regions a Rob suggested, but then do
a binary fill of the blue regions, and use the green (without dilating) as
seeds for the reconstruction. That way you reconstruct the filled blue regions
that have green "inside" them, but not the ones that touch (there aren't any
in the image, but there could be).
If you need the blue regions with a hole where the green region was, just AND
the result of the reconstruction with the firstly segmented blue image.

Another way of resolving this is via region connection calculus
http://www.dentistry.bham.ac.uk/landinig/software/spatial/rcc8d.html
If you separate the blue and green regions in two different binary images and
fill the blue regions, then the green regions are non-tangential proper part
(NTPP relation) of the filled blue regions.

The reference for this is:
Randell DA, Landini, G, Galton A. Discrete Mereotopology for spatial reasoning
in automated histological image analysis. IEEE Trans Patt Rec Mach Intell  
35(3): 568-581, 2013. DOI: 10.1109/TPAMI.2012.128

Hope it is useful.
Regards

Gabriel

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

[Jonas Boehnke]

Thank you very much Gabriel, Sidnei and Rob.

I use Gabrial Landini's binary reconstruct (as described by Rob) and it
works great!
In my case, we analyse gold particles.

Best regards,
Jonas


Am 12.06.2013 14:06, schrieb Rob van 't Hof:

> Hi,
> It is fairly straightforward.  Macro at the end of this email.
> I combined 2 colour thresholds, 1 to find blue objects, and one to
> find green ones, Then I dilated the green objects and used the dilated
> image as a seed in an binary reconstruct operation to find blue
> objects in contact with the green ones. The binary reconstruct plugin
> is from Gabriel Landini's Morpholoy collection of plugins, available
> from his web site here:
> http://www.dentistry.bham.ac.uk/landinig/software/software.html
>
> The colour threshold code is generated by the colour threshold dialog
> by hitting the "Macro" button (you do need to have the macro recorder
> running to record this).
>
> Hope this helps,
>
> Rob
>
> Macro:
>
>
> run("Duplicate...", "title=in1");
> run("Duplicate...", "title=in2");
> selectWindow("in1");
> //First select all blue particles
> // Color Thresholder 1.47t
> // Autogenerated macro, single images only!
> min=newArray(3);
> max=newArray(3);
> filter=newArray(3);
> a=getTitle();
> run("HSB Stack");
> run("Convert Stack to Images");
> selectWindow("Hue");
> rename("0");
> selectWindow("Saturation");
> rename("1");
> selectWindow("Brightness");
> rename("2");
> min[0]=157;
> max[0]=184;
> filter[0]="pass";
> min[1]=47;
> max[1]=255;
> filter[1]="pass";
> min[2]=134;
> max[2]=255;
> filter[2]="pass";
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   setThreshold(min[i], max[i]);
>   run("Convert to Mask");
>   if (filter[i]=="stop")  run("Invert");
> }
> imageCalculator("AND create", "0","1");
> imageCalculator("AND create", "Result of 0","2");
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   close();
> }
> selectWindow("Result of 0");
> close();
> selectWindow("Result of Result of 0");
> rename(a);
> // Colour Thresholding end of autogenerated code-------------
>
> selectWindow("in2");
> //Next select green particles
> // Color Thresholder 1.47t
> // Autogenerated macro, single images only!
> min=newArray(3);
> max=newArray(3);
> filter=newArray(3);
> a=getTitle();
> run("HSB Stack");
> run("Convert Stack to Images");
> selectWindow("Hue");
> rename("0");
> selectWindow("Saturation");
> rename("1");
> selectWindow("Brightness");
> rename("2");
> min[0]=65;
> max[0]=116;
> filter[0]="pass";
> min[1]=101;
> max[1]=255;
> filter[1]="pass";
> min[2]=135;
> max[2]=255;
> filter[2]="pass";
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   setThreshold(min[i], max[i]);
>   run("Convert to Mask");
>   if (filter[i]=="stop")  run("Invert");
> }
> imageCalculator("AND create", "0","1");
> imageCalculator("AND create", "Result of 0","2");
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   close();
> }
> selectWindow("Result of 0");
> close();
> selectWindow("Result of Result of 0");
> rename(a);
> // Colour Thresholding end of autogenerated code-------------
>
> //now find blue objects with green centre
> selectWindow("in2");
> setOption("BlackBackground", true);
> run("Dilate");
> //use binary reconstruct from Gabriel Landini to find blue
> //objects that overlap partially with green inner particles
> run("BinaryReconstruct ", "mask=in1 seed=in2 create white");
> rename("blue particles");
> selectWindow("in2");
> rename("green centers");
> selectWindow("in1");
> close();
>
> On 12/06/2013 11:07, Jonas Boehnke wrote:
>>
>> Hello guys!
>>
>> For sure this is a simple task but I am trying and not getting it done.
>> I want some particles to be selected *by color**treshold*.
>> Please see the excample tiff file attached, it is just an excample to
>> illustrae the principle.
>> I want the large blue particles (including the green inclusions) on
>> the right selected without having the blue on the left side selected...
>>
>> But how?
>>
>> Best regards,
>> Jonas
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Jonas Boehnke]

Hi again!
I got one more thing:

As described by Rob, two images are created, one with "seed" particles
to be dilated and one with "mask" objects. I would like to know the
difference between "seed" and "mask" (in area or pixel or percent or so).
I could simply perform "analyze particles" with both of them and then
substract the second half of particles (see screenshot, particles 6-10)
from the first half (1-5).

It would be much easier to have the difference (in area, pixel or
percent) in the same line with each particle, say instead of "FeretX"
(see screenshot).
I am thinking of how to change the "binary reconstruct" plugin, sothat
the area diffence is not filled white, but say grey and then get a
proportional value by analyzing the "mean grey value" (analyze/set
measurements)

What do you think? And how do I change the plugin to get a grey value
instead of white?

Thank you!
Really great that you spend your free time to help others and me with
such challenges!

Best regards,
Jonas




Am 12.06.2013 14:06, schrieb Rob van 't Hof:

> Hi,
> It is fairly straightforward.  Macro at the end of this email.
> I combined 2 colour thresholds, 1 to find blue objects, and one to
> find green ones, Then I dilated the green objects and used the dilated
> image as a seed in an binary reconstruct operation to find blue
> objects in contact with the green ones. The binary reconstruct plugin
> is from Gabriel Landini's Morpholoy collection of plugins, available
> from his web site here:
> http://www.dentistry.bham.ac.uk/landinig/software/software.html
>
> The colour threshold code is generated by the colour threshold dialog
> by hitting the "Macro" button (you do need to have the macro recorder
> running to record this).
>
> Hope this helps,
>
> Rob
>
> Macro:
>
>
> run("Duplicate...", "title=in1");
> run("Duplicate...", "title=in2");
> selectWindow("in1");
> //First select all blue particles
> // Color Thresholder 1.47t
> // Autogenerated macro, single images only!
> min=newArray(3);
> max=newArray(3);
> filter=newArray(3);
> a=getTitle();
> run("HSB Stack");
> run("Convert Stack to Images");
> selectWindow("Hue");
> rename("0");
> selectWindow("Saturation");
> rename("1");
> selectWindow("Brightness");
> rename("2");
> min[0]=157;
> max[0]=184;
> filter[0]="pass";
> min[1]=47;
> max[1]=255;
> filter[1]="pass";
> min[2]=134;
> max[2]=255;
> filter[2]="pass";
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   setThreshold(min[i], max[i]);
>   run("Convert to Mask");
>   if (filter[i]=="stop")  run("Invert");
> }
> imageCalculator("AND create", "0","1");
> imageCalculator("AND create", "Result of 0","2");
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   close();
> }
> selectWindow("Result of 0");
> close();
> selectWindow("Result of Result of 0");
> rename(a);
> // Colour Thresholding end of autogenerated code-------------
>
> selectWindow("in2");
> //Next select green particles
> // Color Thresholder 1.47t
> // Autogenerated macro, single images only!
> min=newArray(3);
> max=newArray(3);
> filter=newArray(3);
> a=getTitle();
> run("HSB Stack");
> run("Convert Stack to Images");
> selectWindow("Hue");
> rename("0");
> selectWindow("Saturation");
> rename("1");
> selectWindow("Brightness");
> rename("2");
> min[0]=65;
> max[0]=116;
> filter[0]="pass";
> min[1]=101;
> max[1]=255;
> filter[1]="pass";
> min[2]=135;
> max[2]=255;
> filter[2]="pass";
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   setThreshold(min[i], max[i]);
>   run("Convert to Mask");
>   if (filter[i]=="stop")  run("Invert");
> }
> imageCalculator("AND create", "0","1");
> imageCalculator("AND create", "Result of 0","2");
> for (i=0;i<3;i++){
>   selectWindow(""+i);
>   close();
> }
> selectWindow("Result of 0");
> close();
> selectWindow("Result of Result of 0");
> rename(a);
> // Colour Thresholding end of autogenerated code-------------
>
> //now find blue objects with green centre
> selectWindow("in2");
> setOption("BlackBackground", true);
> run("Dilate");
> //use binary reconstruct from Gabriel Landini to find blue
> //objects that overlap partially with green inner particles
> run("BinaryReconstruct ", "mask=in1 seed=in2 create white");
> rename("blue particles");
> selectWindow("in2");
> rename("green centers");
> selectWindow("in1");
> close();
>
> On 12/06/2013 11:07, Jonas Boehnke wrote:
>>
>> Hello guys!
>>
>> For sure this is a simple task but I am trying and not getting it done.
>> I want some particles to be selected *by color**treshold*.
>> Please see the excample tiff file attached, it is just an excample to
>> illustrae the principle.
>> I want the large blue particles (including the green inclusions) on
>> the right selected without having the blue on the left side selected...
>>
>> But how?
>>
>> Best regards,
>> Jonas
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Jonas Boehnke]

Am 18.06.2013 00:24, schrieb Jonas Boehnke:

> Hi again!
> I got one more thing:
>
> As described by Rob, two images are created, one with "seed" particles
> to be dilated and one with "mask" objects. I would like to know the
> difference between "seed" and "mask" (in area or pixel or percent or so).
> I could simply perform "analyze particles" with both of them and then
> substract the second half of particles (see screenshot, particles
> 6-10) from the first half (1-5).
>
> It would be much easier to have the difference (in area, pixel or
> percent) in the same line with each particle, say instead of "FeretX"
> (see screenshot).
> I am thinking of how to change the "binary reconstruct" plugin, sothat
> the area diffence is not filled white, but say grey and then get a
> proportional value by analyzing the "mean grey value" (analyze/set
> measurements)
>
> What do you think? And how do I change the plugin to get a grey value
> instead of white?
>
> Thank you!
> Really great that you spend your free time to help others and me with
> such challenges!
>
> Best regards,
> Jonas
>
>
>
>
> Am 12.06.2013 14:06, schrieb Rob van 't Hof:
>> Hi,
>> It is fairly straightforward.  Macro at the end of this email.
>> I combined 2 colour thresholds, 1 to find blue objects, and one to
>> find green ones, Then I dilated the green objects and used the
>> dilated image as a seed in an binary reconstruct operation to find
>> blue objects in contact with the green ones. The binary reconstruct
>> plugin is from Gabriel Landini's Morpholoy collection of plugins,
>> available from his web site here:
>> http://www.dentistry.bham.ac.uk/landinig/software/software.html
>>
>> The colour threshold code is generated by the colour threshold dialog
>> by hitting the "Macro" button (you do need to have the macro recorder
>> running to record this).
>>
>> Hope this helps,
>>
>> Rob
>>
>> Macro:
>>
>>
>> run("Duplicate...", "title=in1");
>> run("Duplicate...", "title=in2");
>> selectWindow("in1");
>> //First select all blue particles
>> // Color Thresholder 1.47t
>> // Autogenerated macro, single images only!
>> min=newArray(3);
>> max=newArray(3);
>> filter=newArray(3);
>> a=getTitle();
>> run("HSB Stack");
>> run("Convert Stack to Images");
>> selectWindow("Hue");
>> rename("0");
>> selectWindow("Saturation");
>> rename("1");
>> selectWindow("Brightness");
>> rename("2");
>> min[0]=157;
>> max[0]=184;
>> filter[0]="pass";
>> min[1]=47;
>> max[1]=255;
>> filter[1]="pass";
>> min[2]=134;
>> max[2]=255;
>> filter[2]="pass";
>> for (i=0;i<3;i++){
>>   selectWindow(""+i);
>>   setThreshold(min[i], max[i]);
>>   run("Convert to Mask");
>>   if (filter[i]=="stop")  run("Invert");
>> }
>> imageCalculator("AND create", "0","1");
>> imageCalculator("AND create", "Result of 0","2");
>> for (i=0;i<3;i++){
>>   selectWindow(""+i);
>>   close();
>> }
>> selectWindow("Result of 0");
>> close();
>> selectWindow("Result of Result of 0");
>> rename(a);
>> // Colour Thresholding end of autogenerated code-------------
>>
>> selectWindow("in2");
>> //Next select green particles
>> // Color Thresholder 1.47t
>> // Autogenerated macro, single images only!
>> min=newArray(3);
>> max=newArray(3);
>> filter=newArray(3);
>> a=getTitle();
>> run("HSB Stack");
>> run("Convert Stack to Images");
>> selectWindow("Hue");
>> rename("0");
>> selectWindow("Saturation");
>> rename("1");
>> selectWindow("Brightness");
>> rename("2");
>> min[0]=65;
>> max[0]=116;
>> filter[0]="pass";
>> min[1]=101;
>> max[1]=255;
>> filter[1]="pass";
>> min[2]=135;
>> max[2]=255;
>> filter[2]="pass";
>> for (i=0;i<3;i++){
>>   selectWindow(""+i);
>>   setThreshold(min[i], max[i]);
>>   run("Convert to Mask");
>>   if (filter[i]=="stop")  run("Invert");
>> }
>> imageCalculator("AND create", "0","1");
>> imageCalculator("AND create", "Result of 0","2");
>> for (i=0;i<3;i++){
>>   selectWindow(""+i);
>>   close();
>> }
>> selectWindow("Result of 0");
>> close();
>> selectWindow("Result of Result of 0");
>> rename(a);
>> // Colour Thresholding end of autogenerated code-------------
>>
>> //now find blue objects with green centre
>> selectWindow("in2");
>> setOption("BlackBackground", true);
>> run("Dilate");
>> //use binary reconstruct from Gabriel Landini to find blue
>> //objects that overlap partially with green inner particles
>> run("BinaryReconstruct ", "mask=in1 seed=in2 create white");
>> rename("blue particles");
>> selectWindow("in2");
>> rename("green centers");
>> selectWindow("in1");
>> close();
>>
>> On 12/06/2013 11:07, Jonas Boehnke wrote:
>>>
>>> Hello guys!
>>>
>>> For sure this is a simple task but I am trying and not getting it done.
>>> I want some particles to be selected *by color**treshold*.
>>> Please see the excample tiff file attached, it is just an excample
>>> to illustrae the principle.
>>> I want the large blue particles (including the green inclusions) on
>>> the right selected without having the blue on the left side selected...
>>>
>>> But how?
>>>
>>> Best regards,
>>> Jonas
>>>
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>

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