Installation

From Napari interface

EpiCure is a Napari plugin, in python. You can install it either through an already installed Napari instance by going in Napari to Plugins>Install/Uninstall, search for Epicure and click Install. You could have version issues between the different modules installed in your environment and EpiCure dependencies, in this case it is recommended to create a new virtual environnement specific for EpiCure.

From a virtual environment (recommended)

To install EpiCure in a new environnement, you should create a new virtual environnement or activate an exisiting compatible one.

Step 1 : install a Python management package (if you don't have one already).

You have different options, but you have to choose one:

Miniforge (recommended): fast, free but no interface. Follow the detailled steps here to install miniforge
venv: fast and simple install in general, no interface. See tutorial here
Mamba: fast, free but no interface. See here
Anaconda: a sort of interface, works well on MacOS and Windows but slow and might not stay free to all. See here: on windows, on macOS or on linux ).

Step 2 : Create a virtual environment with that python management package.

Once you have installed such Python management package, they generally create one environment called base but you should not install anything in that environment.

You need to create an environment where you will install EpiCure. To do so you first open the terminal (activated in the base environment), and type:
```
    conda create -n epicurenv python=3.10
```
It will install python 3.10 and create an environment called epicurenv.

Python version

If you wish to use the option to segment the movie with Epyseg, you must use a python version until <= 3.10. Indeed, epyseg is not compatible on more recent versions. By default, we recommend 3.10 so that everything is compatible

Step 3: Install EpiCure

Once you have created/identified a virtual environnement, type in the terminal:

conda activate epicurenv

to activate it (and start working in that environnement).

Type in the activated environnement window:

pip install epicure

to install EpiCure with its dependencies.

**Step 4: Open napari and start using EpiCure ** You can open napari by writing napari in the terminal. It is often slow to open the first time but that’s it.

You can start EpiCure by going in Plugins>EpiCure>Start Epicure and follow the Usage online documentation to know how to use it.