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Tests

Plot tissue asymmetry

Overview

Quantifies and plots 3D posterior neural fold asymmetry in confocal images of mice embryos.

Unprocessed PNP & Distance Map Median differences of both WT and MT embryos Median difference image rotated Areas in which there is significant asymmetry Significant asymmetry image rotated

version number: 1.0.1 author: Henry Crosswell

Usage:

Disclaimer: This technique has only been tested on confocal images of the posterior neural folds of E9 mice.

Step 0

To prepare the images before analyse, the following macros must be used on ImageJ.

Images must all be resized within the same dimensions.

Step 1

Create a new folder and place all images to be quantified within. Create another new folder, this will be where your plots are saved.

Image naming conventions:

  • Wild-type embryo images must begin with "WT image".
  • Excluded images must begin with "CF+ image".
  • Other included images can remain unspecified

Step 2 - Installation

Install the scipt!

  1. Create a conda environment, with the dependencies listed in environment.yml.
conda env create
  1. A new conda environment named asymmetry, which will be activated before use:
conda activate asymmetry
  1. Install tissue_asymmetry_python next.
pip install tissue_asymmetry_python

Step 2.5 - customise main.py

Within the main.py file, you can customise the elevation and azimuth of your final plots. //could also be prompted in terminal so this editing script isn't necessary

Step 3 - Run the script

From your terminal, type:

python main.py

Step 4

Now follow the steps prompted by the terminal.

  1. It will first ask you to select a folder, make sure to select the folder with the pre-named images within.
  2. Next it will ask for an output folder for your saved images, select the one created earlier.

Contributors

Henry Crosswell Dr. Alessandro Felder