hesperos 0.1.23

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
  • Upgrade Hesperos version
• Hesperos: Manual Segmentation and Correction
  • Load your image

Installation and Requirements

Hesperos plugin is designed to run on Windows operating system and 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 script_files folder, for Windows or Macos.

3. Add the Anaconda path in these script files:

   1. For Windows: Right click on the .bat files (for installation and running) and select Modify. Change PATH_TO_ADD with 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 PATH_TO_ADD with your Anaconda 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 virtual environment in Anaconda with python 3.9 and Napari 0.4.14. /!\ Hesperos plugin is not yet compatible with Napari version superior to 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. On Napari, use the hesperos plugin with Plugins/hesperos.

Manual installation

1. Install Anaconda and deselect Add to PATH.

2. Open your Anaconda prompt command.

3. Create a virtual environment with Python 3.8, 3.9 or 3.10 :

   $ conda create -n hesperos_env python=3.9

4. Install Python packages (in your virtual environment):

   $ conda activate hesperos_env

   $ conda install -c conda-forge napari=0.4.14 /!\ Hesperos plugin is not yet compatible with napari version superior to 0.4.14.

   $ conda install -c anaconda pyqt if needed

   $ pip install hesperos

5. Launch Napari:

   $ napari

Upgrade Hesperos version

1. Double click on the run_hesperos file to run Napari.
2. On Napari:
   1. Go to Plugins/Install Plugins...
   2. Search for "hesperos" (it can take a while to load).
   3. Click on Update if a new version of Hesperos have been found. You can check the last version of Hesperos in the Napari Hub.
   4. When installation is done, close Napari. A restart of Napari is needed to take in consideration the new installed plugin.

Hesperos: Manual Segmentation and Correction

Loading panel

Hesperos plugin can be used with Digital imaging and communications in medicine (DICOM), Neuroimaging Informatics Technology Initiative (NIfTI) or Tagged Image File Format (TIFF) images. To improve performances, use images that are located on your disk.

To load a image file (.tiff, .tif, .nii or .nii.gz) use the IMAGE button. To load a unique DICOM serie use the IMAGE button. Folder with multiple DICOM series is not supported.

After Loading, a slider appears to zoom in/out on the image. Zoom is also possible with the mouse scroller. If the image is a DICOM serie, a default contrast have the possibility to select a default contrast for the image (to highlight bones or soft tissues according to their Hounsfield Units.)

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