Welcome to imagej_macros_and_scripts Discussions! #5
Replies: 11 comments 10 replies
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Hi Volker, |
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or could you maybe provide me a sample image, so I can check, if maybe the input file is the issue and not the tool itself? |
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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 Volker, Thanks for your support! Best,
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I just tried to analyze my input files on a windows PC with ImageJ and the mri wound healing tool and still did not work out. |
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Hi @skanda58, I see that you opened the image as virtual stack, although this works it is not helpful for the tool, since the image is duplicated before processing anyway and therefore completely loaded into memory. Your own images do not look like images for the tool. For the tool apart from the gap there should be tissue in the image everywhere. Still by cropping and using the right parameters it could work. If you can provide an original input image (not a screenshot) I can try. |
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Hello, I am interested in your tool to identify layer and measure their thickness which is SkinTool. I managed to use your plugin for one channel and measure one layer but it does not work for others. Is there any possibility to use it for my analysis ? ( I attached an image to show) Thank you for your help ! |
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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 @Svethna, |
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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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Hello, what you did is wonderfull. I tested it but the same error is coming, whether I test it on my images or even on the dataset included in the plugin. I have the latest version with all the plugins that are required installed. I can successfully use the "local thickness" tool or the voronoi but when i want to use "perpendicular to inertia axis" this error codes comes up : Can you please help me to solve it ? Thanks once again for your kind help. |
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Hi @Svethna, If there should be anymore problems, you encounter, I would aks you to create an Issue, rather than reporting it here. Best, |
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Hi,
What should I do? |
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Hi @Clairedf, |
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Hi, |
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Hi, |
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Hi @chaipotter,, usually we apply the Wound Healing Tool on a time-series (in the form of a stack, i.e. one image with many frames). In that case each xls-files will contain one line per frame. It seems that you have images with just one frame, why is that? Is that the individual frames of a time-series or are that independent images? In the first case, you could import them all as a stack into ImageJ and run the Wound Healing Tool on that. Best, |
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