Using ImageJ software to measure branch numbers and branch length of Neurons and install plugins
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- เผยแพร่เมื่อ 18 ส.ค. 2022
- This video also shows how to install Analyze Skeleton plugins into ImageJ software
Link to the plugins
github.com/fiji/AnalyzeSkelet...
Thank you for the video !! you just solved a major problem for me!
Great to know that you found it useful.
Very helpful Nandu bhaiyya...I am Pradipta from NCCS Pune..I am currently doing analysis of confocal images in ImageJ..
Hello Pradipta, hope the ImageJ videos you found in my TH-cam channels are useful. Let me know what type of analysis you perform. May be I can upload more tutorials.
Thanks for the video. can you please make a video on how to do analysis of CAM angiogenesis using Image J vessel analysis plug-in.
Hello. thanks for the suggestion and watching my video. Unfortunately I do not have an image of CAM angiogenesis. If you intend to measure vascular density or diameter please check this video th-cam.com/video/3VZ_Qjvmh64/w-d-xo.html FYI there is another video where the neuron length has been measured th-cam.com/video/fcqNutzR7F4/w-d-xo.html hope you find these useful
@@nrttaye4033 Thank you..😊
Thank You for video, your video is highly informative. Here I have a question "weather the same strategy can be used for the quantification of angiogenesis?"
Glad you found it useful. i am currently making a video tutorial on angiogenesis (tube formation) using huvec cells. i found the strategy is quite different. probably in a 2 weeks time the video should be available.
Hello, the video for quantification of angiogenesis is now available. Here is the link. th-cam.com/video/sQLYoJxgUCk/w-d-xo.html
Does this work with a file with multiple z-stacks? or only in maximum projection format? Again, I find it helpful with blood vessels, because the other video that you beautifully showed how to quantify blood vessels, didn't capture branching, or touriousity. Thanks a lot
Hello, you are welcome. Glad you found the video helpful. This approach is applicable to branching structures like neurons, blood vessels, lymph nodes, glands, plant roots, and other filamentous structures. i tired with a zstacked image and it works. I believe that results may vary depending on the projections chosed such as average intensity, maximum intensity, minimum intensity, sum slices, standard deviation, and median.
Hi! Im wondering what is the definition of a "complete skeleton". For example # branches analyzes the number of branches on a complete skeleton, but what is that exactly?
Hello, thanks for reaching out to @nrtTAYE. once the image is under process, binary and skeletonize, the neurons are converted into one/many discrete lines with a known start and end position (see video at 2:25 mins) depending on the "connections" of the neurons. one of these form the complete skeleton.
Hi, Im following all the instructions but the result table does not show after I do the anlayze skeleton. What could I be doing wrong do you have an idea? Thank you.
Hello, I am not quite sure about it. It happens when the threholding (red) is mismatched with the foreground/background color. for instance, after binary the thresholded part may need to be black foreground with a white background. If you can send me a sample image I can get back to you after troubleshooting.
Thank you for the tutorial. It is very helpful. Can you please make a tutorial on measuring mitochondrial network morphology analysis (MiNA) image j tool?
Thank you for your consideration!!
hello. glad you found it helpful. i could try making a tutorial about MINA. However, i do not have an image. do let me know if you have a spare image for making the tutorial. thanks
Hello thanks for your nice explanation, I saw in another tutorial they calculate the ratio of end point voxel to Soma.. Can you explain what information we can get from that calculation? Thanks
Hello! I am wondering how this could be used in conducting angiogenesis analysis with results from CAM Assay. Thank you
Hello, i replied to your other comment that may contain info about CAM analysis. Hope you find it useful