Posted by
CARL Philippe (LBP) on
Oct 25, 2018; 1:24pm
URL: http://imagej.273.s1.nabble.com/problem-with-summary-and-results-windows-slice-and-label-not-appear-tp5021348p5021351.html
Dear Patricia,
> I am well aware of everything you list but the problem is recent (less than a month).
Did you try to make "inverse updates" of your ImageJ software by doing "Help->Update ImageJ..." and choosing an older version to check whether your code is working as you expect it with older installs?
And if the outcome is not positive, then your issue is not due to an ImageJ update, but maybe either your data or different options settings.
My best regards,
Philippe
-----Message d'origine-----
De : ImageJ Interest Group [mailto:
[hidden email]] De la part de OBEID Patricia 154904
Envoyé : jeudi 25 octobre 2018 14:41
À :
[hidden email]
Objet : Re: problem with summary and results windows : "slice" and "label" not appear
Thank you Michael,
I am well aware of everything you list but the problem is recent (less than a month).
I want to attach 2 images for test but I do not know how to do? It's about counting the nuclei.
You wrote "I also do not understand why you measure 'mean' and 'min' after" Convert to Mask. "After that step, the particles have a uniform pixel value of 255. If you want to measure the mean and min pixel Rating of your particles, run "Analyze Particles" on the thresholded image, not on the mask. "
I'm doing this because I only want to record the number of nuclei. The intensities are not useful to me.
Thanks again
Patricia
-----Message d'origine-----
De : ImageJ Interest Group <
[hidden email]> De la part de Michael Schmid
Envoyé : jeudi 25 octobre 2018 14:12
À :
[hidden email]
Objet : Re: problem with summary and results windows : "slice" and "label" not appear
Hi Patricia,
Maybe your images have only one slice?
If there is only one slice, the 'label' comes from the title of the image. With
run("Duplicate...", "title=[] use");
you specify that the title is blank.
If there are several slices, the label (and the 'slice' column of the
Summary) comes from the slice name; if it is empty it indicates that the slice names are empty. You can see the slice names below the title bar of an image, e.g.
5/15 (mySliceNameFive); 512x512 pixel; 8-bit
Anyhow, I don't understand why you duplicate the images in the macro; even if you modify them with "Convert to Mask", nothing will happen to the image files as long as you don't save the modified images.
I also don't understand why you measure 'mean' and 'min' after "Convert to Mask". After that step, the particles have a uniform pixel value of 255. If you want to measure the mean and min pixel values of your particles, run "Analyze Particles" on the thresholded image, not on the mask.
Michael
________________________________________________________________
On 25/10/18 13:46, OBEID Patricia 154904 wrote:
> Dear all,
> Since few days, the column < slice > from window < Summary > and < label > from window < Results > stay empty.
> I use macros that I run regularly and that did not pose a problem
> Today these columns remain empty.
> I am using version 1.52h
> Here is my macro:
>
> dir = getDirectory("Choose a Directory ");
> dir2 = getDirectory("Choose Destination Directory ");
>
> list = getFileList(dir);
> setBatchMode(true);
> for (i=0; i<list.length; i++) {
> if (endsWith(list[i], "d0.C01")){
> path = dir+list[i];
> open(path);
> run("Duplicate...", "title=[] use");
> run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
> run("Set Measurements...", "area mean standard min display redirect=None decimal=2");
> setAutoThreshold("Li dark");
> run("Convert to Mask");
> run("Analyze
> Particles...", "size=20-200 pixel circularity=0.00-1.00 show=Nothing
> display summarize add");
>
> run("Close All");
> if (roiManager("count")>0) roiManager("reset");
>
> }
> }
>
> selectWindow("Summary");
> saveAs("Text",dir2+"Comptage.xls");
> run("Close");
> ........................................................................................................................
> I can not identify where the problem is.
> Thank you for your help
> Patricia
>
>
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