Prerequisites

Before running this project, ensure that you have the following installed:

• Python: Make sure Python is installed on your system. You can download it from the official Python website. Install Python 3.11 and up.

To verify your Python installation, run:

python --version

or for some systems:

python3 --version

Folder structure

The images of the embryo for a given focal plane should be pasted into the corresponding focal folder located in "all_data_first". Here is an example for one of the focal planes:

GUI

The current state of the code does not provide a GUI, meaning that a basic understanding of Python is needed in order to apply changes to the algorithm and run it. Comments have been provided in all major parts of the code.

Current parameter settings

Currently, the code runs a hardcoded combination of parameters (as we have already calculated the parameter leaderboard). If you would like to recalculate the metric evaluation for all 900 combinations, please uncomment the relevant code on lines 845-863

Installation Instructions

1. Clone the repository and navigate to the project directory:

   git clone <repository_url>
   cd <repository_directory>

2. Install the required dependencies by running:

   pip install -r requirements.txt

Optional Step

If you'd like to ensure your pip is updated before installing dependencies, you can use the following command:

pip install --upgrade pip && pip install -r requirements.txt

This will upgrade pip to the latest version and then install the required dependencies.