TR: Threshold doesn’t apply because of Threshold not set error
Locked
TR: Threshold doesn’t apply because of Threshold not set error
 
|
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 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]<mailto:[hidden email]> Tél : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 Toute notre actualité 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 également 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 |
image001.jpg (11K) |
|
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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 > > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 > > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 > > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
|
|
In reply to this post by OBEID Patricia 154904
Greetings Patricia,
and thanks for making the sample images accessible! "When I do an AutoThreshold on the .C01 image, I have an error when I click Apply: "Threshold is not set"." Import of the .C01 image per Bio-Formats and applying an automatic threshold work well. No problems so far with plain ImageJ v1.53i on a Mac running Java 1.8.0_271. Regards Herbie ::::::::::::::::::::::::::::::::::::::::::::::::::: -- Sent from: http://imagej.1557.x6.nabble.com/ -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: TR: Threshold doesn’t apply because of Threshold not set error
|
|
In reply to this post by Cardone, Giovanni
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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 > > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: TR: Threshold doesn’t apply because of Threshold not set error
|
|
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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 > > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: TR: Threshold doesn’t apply because of Threshold not set error
|
|
Hi Giovanni
My java library is jdk1.8.0_66 I have the same problem with a fresh copy of fiji (1.53c vs 1.53i). On a different computer, I haven't the problem. It is the same java library and Fiji 1.53c. Do you know where the difference can come from and how I could go back to a configuration where Apply does not generate an error? Thanks a lot Patricia -----Message d'origine----- De : ImageJ Interest Group <[hidden email]> De la part de Cardone, Giovanni Envoyé : mercredi 21 avril 2021 17:54 À : [hidden email] Objet : Re: TR: Threshold doesn’t apply because of Threshold not set error 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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 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 : (+33)4 38 78 47 12 Fax : (+33)4 38 78 59 17 > > 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 > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
«
Return to ImageJ
|
1 view|%1 views
| Free forum by Nabble | Edit this page |