hesperos 0.1.21

A plugin to manually or semi-automatically segment medical data and correct previous segmentation data.

Hesperos plugin for Napari

TODO : DESCRIPTION

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Table of Contents

• Installation and Requirements
  • Automatic installation
  • Manual installation
• Use Hesperos plugin

Installation and Requirements

Hesperos plugin is designed to run on Windows or Macos with python 3.8, 3.9 or 3.10.

Automatic installation

1. Install [Anaconda] and deselect Add to PATH. Note the path where you install anaconda.
2. Download only the installation folder: [script_files]](/script_files)
3. Add Anaconda path:
   1. For Windows: Right click on the .bat files (for installation and running) and select Modify. Change the anaconda_dir to your anaconda path. Then save changes.

      for exemple: $ anaconda_dir=C:\Users\chgodard\anaconda3

   2. For Macos:

      1. Right click on the .command files (for installation and running) and select Open with TextEdit. Change the PATH_TO_ADD with your anaconda3 path. Then save changes.

         for exemple: $ source ~/opt/anaconda3/etc/profile.d/conda.sh

      2. On your terminal allow running of your .command files (change PATH with the path of your .command files) :

         $ chmod u+x PATH/install_hesperos_env.command

         $ chmod u+x PATH/run_hesperos.command

4. Double click on the install_hesperos_env file to create a anaconda virtual environment with python 3.9 and napari 0.4.14
5. Double click on the run_hesperos file to run napari from your virtual environment.
6. On Napari:
   1. Go to Plugins/Install Plugins...
   2. Search for "hesperos" (it can take a while to load).
   3. Install hesperos plugin.
   4. When installation is done, close Napari. A restart of Napari is needed to take in consideration the new installed plugin.
7. Double click on the run_hesperos file to run napari.
8. Use the hesperos plugin in Plugins/hesperos

Manual installation

1. Install [Anaconda] and deselect Add to PATH. Note the path where you install anaconda.

2. Open your anaconda prompt command

3. Install python 3.8, 3.9 or 3.10

4. Install Python packages (in the conda virtual environment)

   $ conda install -c conda-forge napari=0.4.14

   $ pip install hesperos

5. Launch Napari

   $ napari

Use Hesperos plugin

TODO

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "hesperos" is free and open source software

Anaconda