Semi-manual segmentor

napari widget for semi-manual segmentation of neuronal recordings.

Overview

• A napari widget and supporting utilities for semi-manual segmentation of neuronal recording data.
• Includes example notebook demonstrating a typical segmentation workflow: Segmentation_Example.ipynb

Requirements

• mamba (recommended) or conda
• A working Python environment compatible with the repository (see python_env.yaml)

Installation (mamba)

1. Clone the repository (if you haven't already):

   git clone https://github.com/EmeEmu/semi_manual_segmentor.git
   cd semi_manual_segmentor

2. Create the environment from the provided YAML:

 mamba env create -f python_env.yaml

3. Activate the environment (use the name defined in python_env.yaml):

 mamba activate OrganoidProjectEnv

Quickstart

Notebook (recommended)

1. Activate the environment (see Installation).
2. Start JupyterLab or Jupyter Notebook:
   jupyter lab
   or
   jupyter notebook
3. Open the tutorial notebook: Segmentation_Example.ipynb
4. Run the cells in order — the notebook demonstrates loading data, using the semi-manual segmentation widget, and exporting segmentation results.

Contributing

• Bug reports, feature requests, and pull requests are welcome.
• Please include a clear description of changes, steps to reproduce (for bugs), and tests where applicable.
• If there is no contribution guide in the repo, open an issue to discuss larger changes before implementing them.

Contact / Maintainers

• Repo: https://github.com/EmeEmu/semi_manual_segmentor
• For questions, issues, or requests: open an issue in the repository.