I am approaching dendritic spine density analysis for the first time. I was wondering if there is a way to do it automatically with FIJI, if there is a plugin, I have read some papers, but some do it manually, which I would not , others with softwares different from image j.
If there is a method to do it with image j? I have confocal z-stacks images at 100X
You might consider the Analyze skeleton plugin:
Thanks for you suggestion. I am looking into it, but I am not really getting how this would count spines. From what I am reading in the link you sent AnalyzeSkeleton would skeletonize my image and allow to oount and measure branches, endpoints and juntions, but not spines along the neuron.
Is there something I am missing?
I would recommend you to include example images so that
all forum users can present their best ideas for a possible help.
here it is. Pyramidal neurons imaged at 100X using Golgi staining
I went to a conference last year where I learned about SpineYolo during the poster session. It can do what you want. It isn’t a FIJI plug-in though
Hi Marta, I did a macro in ImageJ/ Fiji for teams in my lab to analyse goldi stainings. If you agree I may try it on your images.
Thank you for sharing this, I am going to look into it to see if it works for me
I would really appreciate that! Have you published it yet? So I could cite it if it will work for my images. I uploaded one of my image, could you try it on that and in case it works share the method?
Hi Marta, Ok, could you send me the link to get the image, I was not able to download it. Maybe it’s somewhere in the paper of a team but without details. if it works on your images I will share it. Best regards, Frédéric