Color thresholding (180-255 of L* value) and obtain L*a*b* values using a macro

[Rie Sadohara]

Dear all,

I am trying to run color thresholding to my image (I want to pick up
180-255 of L* value), converting it to Lab stack, restore selection, and
measure stack (obtain L*, a*, b* value). I recorded macro so that I can do
this in a streamlined way. Please see below. This macro returns a messgae
saying "Supported conversions: 8-bit -> 16 bit* etc...". It seems it cannot
convert the image to Lab stack after color thresholding, but I do not know
why it cannot reproduce what I can run manually. I would appreciate your
help with debugging this code.

run("Color Threshold...");
// Color Thresholder 1.52h
// Autogenerated macro, single images only!
min=newArray(3);
max=newArray(3);
filter=newArray(3);
a=getTitle();
call("ij.plugin.frame.ColorThresholder.RGBtoLab");
run("RGB Stack");
run("Convert Stack to Images");
selectWindow("Red");
rename("0");
selectWindow("Green");
rename("1");
selectWindow("Blue");
rename("2");
min[0]=180;
max[0]=255;
filter[0]="pass";
min[1]=0;
max[1]=255;
filter[1]="pass";
min[2]=0;
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-------------
run("Lab Stack");
run("Restore Selection");
run("Measure Stack");





Thank you.

Rie

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[Gabriel Landini]

On Monday, 5 November 2018 22:34:12 GMT [hidden email] wrote:

> Dear all,
>
> I am trying to run color thresholding to my image (I want to pick up
> 180-255 of L* value), converting it to Lab stack, restore selection, and
> measure stack (obtain L*, a*, b* value). I recorded macro so that I can do
> this in a streamlined way. Please see below. This macro returns a messgae
> saying "Supported conversions: 8-bit -> 16 bit* etc...". It seems it cannot
> convert the image to Lab stack after color thresholding, but I do not know
> why it cannot reproduce what I can run manually. I would appreciate your
> help with debugging this code.

Here is a way of getting the Lab stack and the selection. Note that it reloads
the image.

// Color Thresholder 1.52i
// Autogenerated macro, single images only!
min=newArray(3);
max=newArray(3);
filter=newArray(3);
a=getTitle();
call("ij.plugin.frame.ColorThresholder.RGBtoLab");
run("RGB Stack");
run("Convert Stack to Images");
selectWindow("Red");
rename("0");
selectWindow("Green");
rename("1");
selectWindow("Blue");
rename("2");
min[0]=180;
max[0]=255;
filter[0]="pass";
min[1]=0;
max[1]=255;
filter[1]="pass";
min[2]=0;
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-------------
setOption("BlackBackground", true);
run("Convert to Mask");
run("Create Selection");
run("Revert");
run("Lab Stack");
run("Restore Selection");

The other simpler way of doing this is to just convert your image to Lab, then
threshold the first slice (which is L) with the greyscale thresholder and call
createSelection, no need to use the colour thresholder.

Hope it helps.

Gabriel

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[Rie Sadohara]

Dear Gabriel,

It worked! I would not have been able to figure this out by myself. Thank
you so much for your help!

Rie


On Tue, 6 Nov 2018 at 04:12, Gabriel Landini <[hidden email]> wrote:

> On Monday, 5 November 2018 22:34:12 GMT [hidden email] wrote:
> > Dear all,
> >
> > I am trying to run color thresholding to my image (I want to pick up
> > 180-255 of L* value), converting it to Lab stack, restore selection, and
> > measure stack (obtain L*, a*, b* value). I recorded macro so that I can
> do
> > this in a streamlined way. Please see below. This macro returns a messgae
> > saying "Supported conversions: 8-bit -> 16 bit* etc...". It seems it
> cannot
> > convert the image to Lab stack after color thresholding, but I do not
> know
> > why it cannot reproduce what I can run manually. I would appreciate your
> > help with debugging this code.
>
> Here is a way of getting the Lab stack and the selection. Note that it
> reloads
> the image.
>
> // Color Thresholder 1.52i
> // Autogenerated macro, single images only!
> min=newArray(3);
> max=newArray(3);
> filter=newArray(3);
> a=getTitle();
> call("ij.plugin.frame.ColorThresholder.RGBtoLab");
> run("RGB Stack");
> run("Convert Stack to Images");
> selectWindow("Red");
> rename("0");
> selectWindow("Green");
> rename("1");
> selectWindow("Blue");
> rename("2");
> min[0]=180;
> max[0]=255;
> filter[0]="pass";
> min[1]=0;
> max[1]=255;
> filter[1]="pass";
> min[2]=0;
> 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-------------
> setOption("BlackBackground", true);
> run("Convert to Mask");
> run("Create Selection");
> run("Revert");
> run("Lab Stack");
> run("Restore Selection");
>
> The other simpler way of doing this is to just convert your image to Lab,
> then
> threshold the first slice (which is L) with the greyscale thresholder and
> call
> createSelection, no need to use the colour thresholder.
>
> Hope it helps.
>
> Gabriel
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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*Rie** Sadohara  *
Graduate Research Assistant
Department of Plant, Soil and Microbial Sciences
Michigan State University
Plant and Soil Science Building
1066 Bogue St, Room A364
East Lansing, MI 48824
Email: *[hidden email] <[hidden email]>*
Find delicious bean recipes here:
*https://colorfulhealthfulflavorfulblog.wordpress.com/
<https://colorfulhealthfulflavorfulblog.wordpress.com/>*
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