Installation¶

The linc-convert package is available through multiple installation methods. Note that the package is not yet available on PyPI, so all installation methods install directly from the GitHub repository.

Installation with pip¶

(Optional) Create a new environment

conda create -n linc-convert python=3.11

(Optional) Activate the environment
```
conda activate linc-convert
```
Install the linc-convert package in your environment
```
pip install "linc-convert[all] @ git+https://github.com/lincbrain/linc-convert.git@main"
```
If you don't want to install all dependencies, you can install the dependencies for your specific use case. Replace all in the above command with:
df for dark-field microscopy
lsm for light-sheet microscopy
psoct for polarization-sensitive optical coherence tomography
wk for Webknossos annotations
ts for the TensorStore backend
Run the command-line interface to ensure that installation was successful
```
linc-convert --help
```
View the list of arguments for a modality by running, for example:
```
linc-convert psoct --help
```
View the full list of parameters by running, for example:
```
linc-convert psoct single_volume --help
```

Installation with pipx¶

pipx installs Python applications in isolated environments, making it ideal for command-line tools like linc-convert.

Install pipx (if not already installed):

python -m pip install --user pipx
python -m pipx ensurepath

Install linc-convert with pipx:

pipx install "linc-convert[all] @ git+https://github.com/lincbrain/linc-convert.git@main"

Verify the installation:
```
linc-convert --help
```

Installation with Docker or Apptainer/Singularity¶

For container-based installations using Docker, Apptainer, or Singularity, please refer to the Container Installation Guide.