disco-wight (or Dwight for short)

is a Detector-Independent quality SCOre WIthout Ground TrutH

This repository contains the scripts used in the paper
A detector-independent quality score for cell segmentation without ground truth in 3D live fluorescence microscopy, Vanaret et al. (2023)

Installation

Major dependancies to be installed are :

• numpy : basic library for array manipulation
• matplotlib : basic library to plot figures
• tifffile : library to read and write tiff images
• napari : 3D image visualizer
• scipy : general library for scientific python
• numba : library to make python fast

From your main Conda environment (or from a custom one), refer to the dependancies' individual documentations to install them. This can usually be done easily using pip.

To install the repositiory package:

# from repo root (the DOT "." is important !!!)
pip install -e .

You also need to install the codebase for the software U-track3D from its repo.

Data

The data used in the paper is available at this [link]. WILL BE MADE AVAILABLE SOON

Usage

In the scripts, replace path_to_root = ... by the path to the data folder.