newimage help

[jpdustin]

Hello,

I am very new to ImageJ and writing macros. I've been slowly piecing together a macro to quantify apoptosis and it looks something like this:

macro "full [1]" {
run("RGB Split");
close();
close();
run("Select All");
run("Copy");
newImage("Counts", "8-bit Black", 1300, 1030, 1);
run("Paste");
run("Subtract Background...", "rolling=5");


//run("Threshold...");
setThreshold(56,255);
setOption("BlackBackground", false);
run("Convert to Mask");

run("Watershed");
run("Analyze Particles...", "size=1-100 circularity=0.00-1.00 show=Nothing display clear");

  }

My questions for this macro are:

1) In the newImage line, I want the name to reflect the original image, e.g. I opened the image, image_1331.tif, and want the new image to reflect that automatically but also have it distinguished with "counts" or something.

2) If I wanted the macro to pause at the setThreshold step to allow me to set a different threshold (even a 1x step for a batch process), how would that go? I may not need to do this because I could use an image to determine a threshold for the entire set, then change the settings.

3) I am having the most difficulty getting the results to save automatically (as you can see by not even having any code here). I have tried several google searches and cannot get any of the suggestions to work. Ultimately, I would like it to save to the folder from which the images were opened, reflect the image name with a .xls or .csv extension, and be able to use it to batch process a large number of images.

Any suggestions/help would be great!

Thanks,
JP

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[Jean-Philippe Grossier]

Hi,

1) get the name of your image and then concatenate in newImage():
2) you may use the "wait(n)", but I am not so sure.
3) getInfo("image.directory") and saveAs("Results", "Results.xls"); should
do the job.


macro "full [1]" {

imgName=getTitle();
dir=getInfo("image.directory");

run("RGB Split");
close();
close();
run("Select All");
run("Copy");
newImage("Counts_"+imgName, "8-bit Black", 1300, 1030, 1);
run("Paste");

run("Subtract Background...", "rolling=5");


//run("Threshold...");
setThreshold(56,255);
setOption("BlackBackground", false);
run("Convert to Mask");

run("Watershed");
run("Analyze Particles...", "size=1-100 circularity=0.00-1.00 show=Nothing
display clear");
saveAs("Results", dir+"Results_"+imgName+".xls");

}

you can also check the built in macro page of imagej website (
http://rsb.info.nih.gov/ij/developer/macro/functions.html)

hope it helps,

Jean-Philippe




2015-08-20 14:52 GMT-04:00 JP Dustin <[hidden email]>:

> Hello,
>
> I am very new to ImageJ and writing macros. I've been slowly piecing
> together a macro to quantify apoptosis and it looks something like this:
>
> macro "full [1]" {
> run("RGB Split");
> close();
> close();
> run("Select All");
> run("Copy");
> newImage("Counts", "8-bit Black", 1300, 1030, 1);
> run("Paste");
> run("Subtract Background...", "rolling=5");
>
>
> //run("Threshold...");
> setThreshold(56,255);
> setOption("BlackBackground", false);
> run("Convert to Mask");
>
> run("Watershed");
> run("Analyze Particles...", "size=1-100 circularity=0.00-1.00 show=Nothing
> display clear");
>
>   }
>
> My questions for this macro are:
>
> 1) In the newImage line, I want the name to reflect the original image,
> e.g. I opened the image, image_1331.tif, and want the new image to reflect
> that automatically but also have it distinguished with "counts" or
> something.
>
> 2) If I wanted the macro to pause at the setThreshold step to allow me to
> set a different threshold (even a 1x step for a batch process), how would
> that go? I may not need to do this because I could use an image to
> determine a threshold for the entire set, then change the settings.
>
> 3) I am having the most difficulty getting the results to save
> automatically (as you can see by not even having any code here). I have
> tried several google searches and cannot get any of the suggestions to
> work. Ultimately, I would like it to save to the folder from which the
> images were opened, reflect the image name with a .xls or .csv extension,
> and be able to use it to batch process a large number of images.
>
> Any suggestions/help would be great!
>
> Thanks,
> JP
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[jpdustin]

Thank you! It worked beautifully. I'll have to play with the threshold to get it to pause until I enter the threshold. This is more for a batch process. Ideally, I would like it to pause for only the first image; once I set the threshold for the first image, I would love it to just process the rest in the batch.

Again, thanks for your help.
JP

[Jean-Philippe Grossier]

you may want to use

waitForUser;

it pauses the macro, displays a dialog box, and the macro proceeds when you
click "ok". You should have time to adjust thresholds.

best,
jp

2015-08-21 9:15 GMT-04:00 jpdustin <[hidden email]>:

> Thank you! It worked beautifully. I'll have to play with the threshold to
> get
> it to pause until I enter the threshold. This is more for a batch process.
> Ideally, I would like it to pause for only the first image; once I set the
> threshold for the first image, I would love it to just process the rest in
> the batch.
>
> Again, thanks for your help.
> JP
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/newimage-help-tp5014083p5014097.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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