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Installation

You can install napari-stitcher via pip:

pip install napari-stitcher

To install latest development version: 

pip install git+https://github.com/multiview-stitcher/napari-stitcher.git

Don't have conda installed?

We recommend using python and napari-stitcher within a conda environment. Follow the instructions below to install conda on your computer.

Installing Python

Overview

This how-to teaches how to install Python on your computer using conda, which is both a

  • environment manager and a
  • package manager.

Instructions

Select the installation instructions for your operating system and processor from the tabs below.

  1. In your web browser, navigate to this download page.
  2. Scroll down to the "Miniforge" header of the "Downloads" section. Click the link to download link for Miniforge-Linux-x86_64.
  3. Open your terminal application
  4. Navigate to the folder you downloaded the installer to (usually this is in your Downloads folder). If the file was downloaded to your Downloads folder, you would enter:
cd ~/Downloads
  1. Execute the installer with the command below. You can use your arrow keys to scroll up and down to read the license agreement and enter "yes" if you agree.
bash Miniforge-Linux-x86_64.sh
  1. After installation, you will be asked if you would like to initialize your terminal with "conda init". Enter "yes" to initalize your terminal.
  2. To verify your installation worked, close your Terminal window and open a new one. You should see (base) to the left of your prompt.

Don't see (base)?

You can manually initialize conda by entering the command below and re-opening your terminal application.

conda init
  1. In your web browser, navigate to this download page.
  2. Scroll down to the "Miniforge" header of the "Downloads" section. Click the link to download link for Miniforge-MacOSX-x86_64.
  3. Open your Terminal (you can search for it in spotlight - cmd + space)
  4. Navigate to the folder you downloaded the installer to (usually this is in your Downloads folder). If the file was downloaded to your Downloads folder, you would enter:
cd ~/Downloads
  1. Execute the installer with the command below. You can use your arrow keys to scroll up and down to read the license agreement and enter "yes" if you agree.
bash Miniforge-MacOSX-x86_64.sh
  1. After installation, you will be asked if you would like to initialize your terminal with "conda init". Enter "yes" to initalize your terminal.
  2. To verify your installation worked, close your Terminal window and open a new one. You should see (base) to the left of your prompt.

Don't see (base)?

You can manually initialize conda by entering the command below and re-opening your terminal application. 

conda init

  1. In your web browser, navigate to this download page.
  2. Scroll down to the "Miniforge" header of the "Downloads" section. Click the link to download link for Miniforge-MacOSX-arm64.
  3. Open your Terminal (you can search for it in spotlight - cmd + space)
  4. Navigate to the folder you downloaded the installer to (usually this is in your Downloads folder). If the file was downloaded to your Downloads folder, you would enter:
cd ~/Downloads
  1. Execute the installer with the command below. You can use your arrow keys to scroll up and down to read it/agree to it.
bash Miniforge-MacOSX-arm64.sh
  1. After installation, you will be asked if you would like to initialize your terminal with "conda init". Enter "yes" to initalize your terminal.
  2. To verify your installation worked, close your Terminal window and open a new one. You should see (base) to the left of your prompt.

Don't see (base)?

You can manually initialize conda by entering the command below and re-opening your terminal application. 

conda init

  1. In your web browser, navigate to this download page.
  2. Scroll down to the "Miniforge" header of the "Downloads" section. Click the link to download link for Miniforge-Windows-x86_64.
  3. Find the file you downloaded (Miniforge-Windows-x86_64.exe) and double click to execute it. Follow the instructions to complete the installation.
  4. Once the installation has completed, you can verify it was correctly installed by searching for the "miniforge prompt" in your Start menu.

Creating a conda environment

  • Create a new conda environment with the necessary packages:

    conda create -n napari-stitcher python=3.10 napari pyqt=5

Opening napari

  1. Open a terminal
  2. Activate the right conda environment: conda activate napari-stitcher in the terminal (MacOS) or Miniconda Prompt (Windows)
  3. Start napari by running napari
  4. Start the plugin in the menu plugins > napari-stitcher > Stitcher
  1. Open the Miniconda Prompt (Windows)
  2. Activate the right conda environment: conda activate napari-stitcher
  3. Start napari by running napari
  4. Start the plugin in the menu plugins > napari-stitcher > Stitcher