Skeltonise image


#1

Hi,
I’m trying to create a skeleton image of a number of microglial cells to use Sholl analysis on. I need to create a 8 bit image grayscale and I have but conversion to binary isnt working. What are the steps to create a cell skeleton?


#2

There is a plugin for Sholl Ananlysis available. Have you read the docs already?:

In addition here a plugin to analyze a skeleton:


https://onlinelibrary.wiley.com/doi/abs/10.1002/jemt.20829


#3

What happens when you try?

The technique I use, I go to image -> adjust -> threshold. Then I set the level I want (which is 0 and 0) then I click apply. Then the ‘convert stack to binary’ dialogue pops up and I uncheck the ‘calculate threshold for each image’ box. Then I apply that and my image is now binary.

The next step I use process->skeletonize. For me, it skeletonizes the black regions. So if my lines are white, then I invert the lut before skeletonizing.


#4

I cant get the dialogue box to pop up. Do you need a certain type of image (grayscale, TIFF ect.)???


#5

To my knowledge, it just needs to be a grayscale image. Although ‘make binary’ seems to “work” for me without a dialogue for single-sliced rgb images. Can you make an example image available some how?