Minimum Setup for opening DICOM files in Napari

if this is not the first time you are using this workflow, skip step 1-5 completely

#All commands in this guide should be executed inside the Miniforge Prompt (Windows) or Terminal (macOS).

(1) First time users of Git

if already have Git installed, skip to step 2

Install Git

Windows

1. Download Git for Windows:

https://git-scm.com/install/windows

2. Run the installer and keep all default settings.

3. Open a terminal (Miniforgeprompt on Windows):

git --version

If a version number is displayed, Git is installed correctly.

macOS

1. Open the Terminal.

2. Open a terminal:

• Windows:
  Click the Start menu, search for "Miniforge Prompt", and open it.

• macOS:
  Press Cmd + Space, type Terminal, and press Enter.

3. Check if Git is already installed:

git --version

• If a version number appears → Git is ready to use.
• If not, macOS will prompt you to install the Command Line Tools. Confirm the installation.

(2) Install Python (Miniforge)

if you already have miniforge installed, skip to step 3

We use Miniforge to manage Python and all required packages.

It's recommended to not install Anaconda or Miniconda for this setup to avoid dependency conflicts.

---

Windows & macOS

1. Download Miniforge:

https://github.com/conda-forge/miniforge/releases/latest

2. Run the installer using the default settings.

3. Open a terminal:

• Windows:
  Click the Start menu, search for "Miniforge Prompt", and open it.

• macOS:
  Press Cmd + Space, type Terminal, and press Enter.

4. Verify the installation:

conda --version

• If a version number appears → ready to use.

(3) Clone the Repository

If you have already cloned the repository, skip to Step 4.

In this step, we will download the GitHub repository to your local machine.

Windows & macOS

If this is your first time using Git, it is recommended to create a dedicated folder for your repositories, for example:

Documents/github-repos

1. Navigate to the directory where you want to store the repository.

2. Open a terminal in that directory.

3. Run:

git clone https://github.com/JoelSchaust/Minimum-Napari-DICOM-setup.git

4. in the terminal, navigate to the project folder

cd Minimum-Napari-DICOM-setup

5. check if everything was downloaded correctly

ls 

• if you get a list of all folders and files -> ready to go

(4) create napari environment

if you already created the environment, skipt to step 5

1. Make sure you are inside the project folder.

2. in the terminal, run the following command to create a new envrinoment

mamba env create -f environment.yml

2. to activate the environment (if succesful, the name of the environment (dicom-napari) should appear in the front of the line in the terminal)

conda activate dicom-napari

4. to open Napari, run

napari

• If an empty Napari window appears then you are ready to go

error on macos (requires pyqt5?)