Dear Aura,

Please view this post: http://www.neurostructural.org/default.asp?page=72957

Maybe help you. 

Best wishes,

Ion.

I'm not familiar with dendritic spine morphology but I read on the web it is about obtaining the length, head diameter and so on, isn't it?

Maybe if you attach and example image, I can try to develop an imageJ plugin

Hi Jesus, thank you for the support! Yes I was thinking the same: I would like to create a plug-in for doing this semi-automatically since I have a set of rules that given the spine length and head/neck diameter can classify the spines in mutually exclusive classes. However I am very new in programming with ImageJ and I am not sure from where to start, do you have any tips? thanks in advance (attached is a binary picture as an example of the data I am working on) 

in the image attached, the sipnes are automatically detected? So the markers point the position of a spine?

no they are not, I have added the arrow heads. My idea was to do something semi-automatic, so to take measure of all the parameters (length and diameters) manually and make the software categorize each spine using a set of rules. 

Finding the spines could be done just by "skeletonizing" (process > binary > skeletonize) the binary image and searching the ending points of the line. There are some problems with the noise and outliers points on the initial image, so probably the number of spines found will be overstimated (see image). Anyway, this could be solved in a later step.

Once the spines are located, some questions arise: how the diameter is defined? and the length?

Hi I am really interested to know whether any of you come up with the plug in for IMAGE J to find out spine length and diameter ?

Hey Aura, did u make this plugin? or did u find it? i would be interested in having it or knowing how to create it

Did u make this plugin?

Hello everyone, we just published a preprint on dendritic spine analysis. Check : https://www.biorxiv.org/content/10.1101/2020.09.12.294546v2 and https://github.com/argunsah/spines . Contact me if you need help :)

Dear Aura

We recently published a freely available ImageJ plugin for analysing dendritic spine morphology in a semi-automated way. It is designed for super-resolution microscopy images, but it should readily accept any kind of images.

Here is a link to the paper describing it, I hope you find it helpful.

Article SpineJ: A software tool for quantitative analysis of nanosca...

Hi Aura,

Do you want 2D analysis or 3D analysis?

For 2D analysis you may check:

https://academic.oup.com/bioinformatics/article/32/16/2490/2240270

https://sites.google.com/site/2dspan/

For 3D analysis you may check:

https://www.nature.com/articles/s41598-018-21753-8

https://sites.google.com/view/3dSpAn/

Jan Tønnesen Ali Özgür Argunşah

I read this paper you published about the SpineJ plugin but to be honest, I would need some help in applying it. I have brightfield pictures (100x) of Golgi stained dendritic segments and would like to quantify spines and analyse morphologies. Do you have a step by step manual for the usage of ImageJ by any chance?

Thanks and kind regards,

Alexandra

Hello,

The one we published in biorxiv (SpineS) is for fluorescent images. The one published by Jan Tønnesen is SpineJ.

If you share some images I can check if there is a way of making SpineS work for those images as well.

Best,

Ali

Ali Özgür Argunşah Thanks for the quick reply =)

I got confused there, I'm sorry. But I attached an example pic =)

Thanks

Hi everyone, i'm using thy-gfp mice in order to do the spine analysis after treatment, i took stacks with confocal microscopy (SP8 from Leica), and i tried the pluggin SpineJ but it didn't recognise my spines and give me always zero for all the parameters. i wanted to know if i can have a more detailed file than the manual published and if it is possible to do the analysis on stacks instead of a single image,

thanks a lot for your reply and help,

Iness

Here is our paper on the analysis of dendritic spines for those who are interested: https://rdcu.be/cR24x

We also have a list of other published tools in the Supplementary Table 1.