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

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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

2. A new conda environment named asymmetry, which will be activated before use:

conda activate asymmetry

3. 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

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Henry Crosswell Dr. Alessandro Felder