# Installation

It is advised to work with a conda environment.

## Installation from yml file
A `environment.yml` is provided. This will install all the dependencies, even the optative ones. If you want to select just some of them, check maual installation.

```bash
conda create -n registration_tools -f environment.yml
```

## Manual installation

Requirements:

Python version:
  - python>=3.11.11

```bash
conda create -n registration_tools python=3.11
conda activate registration_tools #To activate environment
```

Compulsory packages:
  - h5py
  - zarr>=3.0.3
  - scikit-image

```bash
#Assuming you are inside the environment (registration_tools)
conda install h5py zarr>=3.0.3 scikit-image
```

Additional packages
  - vt-python: In case yuo want to register files. Installation docs (here)[https://gitlab.inria.fr/morpheme/vt-python].

```bash
#Assuming you are inside the environment (registration_tools)
conda install vt-python -c morpheme
```

  - napari: If you want to visualize the data. Installation docs (here)[https://napari.org/dev/tutorials/fundamentals/installation.html].
  - pyqt: Required by napari. Other alternatives in napari docs. 

```bash
#Assuming you are inside the environment (registration_tools)
conda install napari pyqt -c conda-forge
conda update napari #From documentation of napari, sometimes help is after installation napari has not find pyqt correctly
```