Welcome to imagej_macros_and_scripts Discussions! #5
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Hi Volker, |
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Hi @skanda58, You can also find two example images on the tool's help-page . If you should still have problems, please send me an image and I will have a look. Best, |
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Hi @Svethna, Should your problem be related to something else, please send me the raw input images, so that I can test. Please also note that it only measures the "thickness" in some sense. The 'm'-button measures vertically across the object from local extrema of the lower border, while the 't'-button measures across the object, perpendicular to the lower border, at random positions. Please let me now if you'd prefer different measurements, I'd be happy to add them. |
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-->Hello, Thank you very much for your fast reply, it is very appreciated. I posted only the region I am interested in measuring parameters. I use images acquired with a microscope with 2 fluorescence channels that I merge with ImageJ. Until now, to use the plugin I would then switch to RGB stack to make a threshold on each channel where each color marks a layer. In my mind, the threshold gives an upper and lower limit of the layer of interest. Then I wanted to make consecutive measurements parallel to each other but perpendicular to the surface, all along the layer. I found that for my green channel I could more or less achieve what I wanted (although I had to resize the image and flip it so that the layer was roughly horizontal, otherwise the measurements were no longer perpendicular to the surface) but I couldn't get a result for the red. I don't know if I'm clear enough, I'm attaching some raw images as well as an image showing my region of interest and I hope you can help me.I really thank you in advance for your time. Please find the files on this wetransfer link : https://we.tl/t-wWkt9BgjXD Have a nice day.Regards, Svethna De : VolkerEnvoyé le :mardi 18 octobre 2022 15:11À : MontpellierRessourcesImagerie/imagej_macros_and_scriptsCc : Svethna; MentionObjet :Re: [MontpellierRessourcesImagerie/imagej_macros_and_scripts] Welcome to imagej_macros_and_scripts Discussions! (Discussion #5) Hi @Svethna,is that the complete image or just a region? You run the tool on a binary mask, so you have to create that first. The tool will (sometimes) not work correctly if the mask touches the upper or lower border of the image. Now the red channel you cannot really analyze, at least not at the left and right parts, because we cannot see the lower border and cannot know the thickness there. Depending on how you segment the green channel, it might touch the upper border, however only minimally, we did not really loose the thickness information, so you can do on the mask of the grreen channel: select all, cut, paste, move it down some pixels. Now it won't touch the border any more and the tool will work.Should your problem be related to something else, please send me the raw input images, so that I can test.Please also note that it only measures the "thickness" in some sense. The 'm'-button measures vertically across the object from local extrema of the lower border, while the 't'-button measures across the object, perpendicular to the lower border, at random positions.Please let me now if you'd prefer different measurements, I'd be happy to add them.Best,Volker—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>
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-->Hi again, As far as I understood, it applies only for 3D images. The skintool had the best result so far that is why I wanted to find a way to apply it to all the layers of my tissue. Regards,Svethna De : VolkerEnvoyé le :mardi 18 octobre 2022 17:03À : MontpellierRessourcesImagerie/imagej_macros_and_scriptsCc : Svethna; MentionObjet :Re: [MontpellierRessourcesImagerie/imagej_macros_and_scripts] Welcome to imagej_macros_and_scripts Discussions! (Discussion #5) Hi @Svethna,why wouldn't you simply use FIJI's local-thickness plugin for that? Make a mask of your region of interest, run the plugin and you will get a table with the thickness values (calculated from the distance map, i.e. perpendicular to the centerline). Does that solve your problem?Best,Volker—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>
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Hi @Svethna, |
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Hello again, I might not be using the Local Thickness plugin the way you did. I end up with this image (after changing type into 8 bit then thresholding to create a mask) giving a visual representation of local thickness I guess. The given value are shown in the table and the histogram but do not correspond of what I expect of layer thickness… Thank you once again for your help. Regards,Svethna De : VolkerEnvoyé le :mardi 18 octobre 2022 17:41À : MontpellierRessourcesImagerie/imagej_macros_and_scriptsCc : Svethna; MentionObjet :Re: [MontpellierRessourcesImagerie/imagej_macros_and_scripts] Welcome to imagej_macros_and_scripts Discussions! (Discussion #5) Hi @Svethna,no, the local thickness also works with 2D images. I just tried it on your image and the result looks fine to me.Please try it. I'm sure it is much closer to what you need than the skin-tool.Best,Volker—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>
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Hi @Svethna |
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Hi, What should I do? |
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Hi, |
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Hi, I'm trying to use the MRI Opera export tools. I read a 96 well plate (48 wells) in the Phenix for alexa 488. I exported the raw tiff files and need to stitch them. However when I installed the plug ins, I'm encountering a IndexError: index out of range: 17 |
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Hi Mr. Volker,
The files are 3.5 GB, please let me know if you have trouble opening them.
These are exports from the OPERA PHENIX. The images are named
row_column_field_channel
I imaged 2 channels.
Your help is greatly appreciated,
Isabel Melo
Images.zip
<https://drive.google.com/file/d/1wlYFP2jIK4TMu-pMF-j_BivtygUe0cNJ/view?usp=drive_web>
El lun, 15 jul 2024 a las 5:57, Volker ***@***.***>)
escribió:
… Hi @isabelmelo16 <https://github.com/isabelmelo16>,
sorry for the late reply, I've been on holiday. I can not tell, without
more information. Could you send the complete output from the log. The best
would be if I could have your dataset to test, if that is possible.
Best,
Volker
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--
*Isabel Melo-Escobar, MS*
Phone: +1 (561)709-9283 | https://orcid.org/0000-0003-3176-9181 | LinkedIn
<https://www.linkedin.com/in/isabel-melo-escobar-ab917b149>
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Hi, I am trying to use the MRI Opera Export Tools but am not having much luck with selecting the index file. I have imported the raw data straight from Harmony and the index file is currently in a .xml file. The index file is able to open normally on ImageJ (without using the export tool files). I am getting the Index File not found! error. The Harmony version is 5.1. I have checked the file path and there are no special characters. I have reinstalled the export files in the toolsets folder but it is still not working. Any help is much appreciated! Thanks :) |
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