SHG Quantification Tools

This code provides tools for quantification of second harmonic generation (SHG) images. Now uses Matlab 2016b runtime

Running the code

Getting started

• To run the code you need Matlab. We have tested the code with version R2015a and above.
• Download the code using git or by clicking 'Download ZIP' on the GitHub project page
• In Matlab, navigate to the shg-quantification-tools folder and type Interface to run the user interface

Intensity analysis of SHG images

Aim

To quantify the average SHG intensity through a series of z-stacks, producing an z-profile of intensity for each stack aligned such that the position of maximum intensity occurs in the same position for each stack.

We currently assume that the z-stacks are saved in a Leica LIF file.

Method

• Acquire a series of z-stacks from one or more samples in a Lif file
• Select the Process SHG from Lif menu item
• Select your Lif file
• Select the correct options for your data
  • Filter using string: If you would only like to process images from the Lif file with a names that contain a string, enter that string in the filter text box. E.g. if you enter SHG, only files containing SHG such as Sample 1 SHG or SHG Slide 1 will be processed.
  • Channel Number (zero-indexed): channel in the data containing the SHG images. If there is only one image, use 0, if you would like to use the second channel, set 1.

Results

The code will produce two CSV files:

• [filename]-z-profile.csv: One column per sample with the average SHG intensity at each z position
• [filename]-z-profile-aligned.csv: One column per sample with the average SHG intensity at each z position aligned such that the maximum z-intensity occurs at the sample position for each sample

GLCM analysis

Aim

To quantify the GLCM parameters for a series of images