Re: TR: Threshold doesn’t apply because of Threshold not set error

Posted by Cardone, Giovanni on Apr 21, 2021; 3:53pm
URL: http://imagej.273.s1.nabble.com/TR-Threshold-doesn-t-apply-because-of-Threshold-not-set-error-tp5024633p5024641.html

Hi Patricia,

nothing seems to point to an issue with the file, but at the same time I cannot think of what could be wrong.
What java library do you have? In Windows you would find it under the directory "Fiji.app\java\win64".
Otherwise I would suggest to try to download a fresh copy of Fiji (just place it in a different directory than the original, e.g. the Desktop) and try to repeat the procedure. And do the same on a different computer, if needed. This should help to understand if the issue is possibly related to the specific installation of the software or to the computer configuration.
I hope it helps.

Giovanni

-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of OBEID Patricia 154904
Sent: Wednesday, April 21, 2021 5:11 PM
To: [hidden email]
Subject: Re: TR: Threshold doesn’t apply because of Threshold not set error

Hi,
Thanks a lot Giovanni.
The error message appear when I click Apply after thresholding Auto.
If I run("Convert to Mask") directly (as you suggested), there is no problem and the macro works.
Then I don't understand why Apply is not successful ... :-( Thanks again Pat _______________________________________

Patricia OBEÏD


-----Message d'origine-----
De : ImageJ Interest Group <[hidden email]> De la part de Cardone, Giovanni Envoyé : mercredi 21 avril 2021 12:54 À : [hidden email] Objet : Re: TR: Threshold doesn’t apply because of Threshold not set error

Hi Patricia,

personally I can't reproduce your error. I tried it on Fiji/ImageJ, Windows OS, using image both imagej 1.53c and 1.53i, with and without the bio-format update site activated.
Below is a script in macro language that reproduces the steps you described. Can you run it and see if you get an error message? Before running it you only need to change the path to your file.

Giovanni

run("Bio-Formats", "open=D:/Downloads/B02f00_DAPI.C01 autoscale color_mode=Colorized rois_import=[ROI manager] view=Hyperstack stack_order=XYCZT"); setAutoThreshold("Default dark no-reset"); setOption("BlackBackground", false); run("Convert to Mask");



-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of OBEID Patricia 154904
Sent: Wednesday, April 21, 2021 11:55 AM
To: [hidden email]
Subject: Re: TR: Threshold doesn’t apply because of Threshold not set error

Good morning all,
The images to illustrate my problem are available here:
http://dl.free.fr/j4PkxOgxz
Thanks a lot
Patricia
_______________________________________

Patricia OBEÏD
Ingénieur de Recherche /Animateur Informatique Biomics Institut de Recherche Interdisciplinaire de Grenoble CEA/DRF/IRIG/DS U1292 /BGE (U1038)/Biomics/Bât 4020
17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat à l'énergie atomique et aux énergies alternatives Email : [hidden email] Tél : [phone]         Fax : [phone]

Toute notre actualité sur www.cea.fr et sur http://www.bge-lab.fr/Pages/Biomics/Presentation.aspx 

Suivez-nous également sur Twitter : @CEA_Recherche et sur https://twitter.com/BiomicsLab


-----Message d'origine-----
De : ImageJ Interest Group <[hidden email]> De la part de Herbie Envoyé : mardi 20 avril 2021 16:07 À : [hidden email] Objet : Re: TR: Threshold doesn’t apply because of Threshold not set error

Greetings Patricia!

"I don't how to send you the .C01 image"

Of course, this is of little help because we are not able to test.

Perhaps you make the image accessible from a cloud service or you just try to change the extension (and tell us)...

Regards

Herbie

:::::::::::::::::::::::::::::::::::::::::::::::::::
Am 20.04.21 um 15:05 schrieb OBEID Patricia 154904:

> Good afternoon all
> I am having a problem that I have never had before ...
> I work from images from Cellomics with a .C01 extension. With Bioformat I search for Cellomics and I can open my images.
> When I do an AutoThreshold on the .C01 image, I have an error when I click Apply: "Threshold is not set".
> Whereas when I do the same on the .tif image everything is fine.
> Can someone help me and tell me what to do to make it work again for .C01 images?
> My imageJ version: 1.53i
> Thank you everyone and have a nice day Patricia
>
> PS : I don t how to send you the .C01 image, it has been rejected because it contains an attachment of type 'APPLICATION/OCTET-STREAM'
> _______________________________________
> [http://www.cea.fr/var/cea/signatures/cea_logo.jpg]<http://www.cea.fr/
> >
>
> Patricia OBE D
> Ing nieur de Recherche /Animateur Informatique Biomics Institut de
> Recherche Interdisciplinaire de Grenoble CEA/DRF/IRIG/DS U1292 /BGE
> (U1038)/Biomics/B t 4020
> 17 rue des martyrs 38054 Grenoble Cedex 9 Commissariat   l' nergie
> atomique et aux  nergies alternatives Email :
> [hidden email]<mailto:[hidden email]>
> T l : ([phone]         Fax : [phone]
>
> Toute notre actualit  sur www.cea.fr et sur
> http://www.bge-lab.fr/Pages/Biomics/Presentation.aspx
> <http://www.cea.fr/drf/big/bge/biomics>
>
> <http://www.cea.fr/>Suivez-nous  galement sur Twitter :
> @CEA_Recherche<https://twitter.com/#!/CEA_Recherche> et sur
> https://twitter.com/BiomicsLab
>
>
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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