CellSeg3D

napari-cellseg3d

Plugin for cell segmentation in 3D

    cellseg3d logo

    Code style: black PyPI Downloads Downloads License: MIT Python Version codecov napari hub

    • A napari plugin for 3D cell segmentation: training, inference, and data review. In particular, this project was developed for analysis of mesoSPIM-acquired (cleared tissue + lightsheet) datasets.

    demo

    Installation

    💻 See the Installation page in the documentation for detailed instructions.

    Documentation

    📚 A lot of documentation is available at https://AdaptiveMotorControlLab.github.io/CellSeg3D

    You can also generate docs by running make html in the docs/ folder.

    Quick Start

    To use the plugin, please run:

    napari

    Then go into Plugins > napari-cellseg3d, and choose which tool to use.

    • Review (label): This module allows you to review your labels, from predictions or manual labeling, and correct them if needed. It then saves the status of each file in a csv, for easier monitoring.
    • Inference: This module allows you to use pre-trained segmentation algorithms on volumes to automatically label cells and compute statistics.
    • Train: This module allows you to train segmentation algorithms from labeled volumes.
    • Utilities: This module allows you to perform several actions like cropping your volumes and labels dynamically, by selecting a fixed size volume and moving it around the image; fragment images into smaller cubes for training; or converting labels from instance to segmentation and the opposite.

    News

    New version : v0.2.0

    • Changed project name to "napari_cellseg3d" to avoid setuptools deprecation
    • Small API changes for training/inference from a script
    • Some fixes to WandB integration ad csv saving after training

    Previous additions :

    • v0.1.2 :Fixed manifest issue for PyPi
    • Improved training interface
    • Unsupervised model : WNet3D
      • Generate labels directly from raw data!
      • Can be trained in napari directly or in Google Colab
      • Pretrained weights for mesoSPIM whole-brain cell segmentation
    • WandB support (install wandb and login to use automatically when training)
    • Remade and improved documentation
      • Moved to Jupyter Book
      • Dedicated installation page, and working ARM64 install for macOS Silicon users
    • New utilities
    • Many small improvements and many bug fixes

    Install note for ARM64 (Silicon) Mac users

    To avoid issues when installing on the ARM64 architecture, please follow these steps.

    1. Create a new conda env using the provided conda/napari_CellSeg3D_ARM64.yml file :

       git clone https://github.com/AdaptiveMotorControlLab/CellSeg3d.git
       cd CellSeg3d
       conda env create -f conda/CellSeg3D_ARM64.yml
       conda activate napari_CellSeg3D_ARM64
    2. Install a Qt backend (PySide or PyQt5)

    3. Launch napari, the plugin should be available in the plugins menu.

    Requirements

    Python 3.8 or 3.9 required. Requires napari, PyTorch and MONAI. Compatible with Windows, MacOS and Linux. Installation should not take more than 30 minutes, depending on your internet connection.

    For PyTorch, please see the PyTorch website for installation instructions.

    A CUDA-capable GPU is not needed but very strongly recommended, especially for training.

    If you get errors from MONAI regarding missing readers, please see MONAI's optional dependencies page for instructions on getting the readers required by your images.

    Quick demo

    After installation, you can run the plugin by running:

        napari

    and launching the plugin from the Plugins menu. You may use the test volume in the examples folder to test the inference and review tools. This should run in far less than five minutes on a modern computer.

    You may also find a demo Colab notebook in the notebooks folder.

    Issues

    Help us make the code better by reporting issues and adding your feature requests!

    If you encounter any problems, please file an issue along with a detailed description.

    Testing

    Before testing, install all requirements using pip install napari-cellseg3d[test].

    pydensecrf is also required for testing.

    To run tests locally:

    • Locally : run pytest in the plugin folder
    • Locally with coverage : In the plugin folder, run coverage run --source=napari_cellseg3d -m pytest then coverage xml to generate a .xml coverage file.
    • With tox : run tox in the plugin folder (will simulate tests with several python and OS configs, requires substantial storage space)

    Contributing

    Contributions are very welcome.

    Please ensure the coverage at least stays the same before you submit a pull request.

    For local installation from Github cloning, please run:

    pip install -e .

    License

    Distributed under the terms of the MIT license.

    "napari-cellseg3d" is free and open source software.

    Acknowledgements

    This plugin was developed by originally Cyril Achard, Maxime Vidal, Mackenzie Mathis. This work was funded, in part, from the Wyss Center to the Mathis Laboratory of Adaptive Intelligence. Please refer to the documentation for full acknowledgements.

    Plugin base

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

    Version:

    • 0.2.0

    Last updated:

    • 13 May 2024

    First released:

    • 25 June 2022

    License:

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 57
    • Forks: 10
    • Issues + PRs: 4

    Python versions supported:

    Operating system:

    Requirements:

    • numpy
    • napari[all]>=0.4.14
    • QtPy
    • scikit-image>=0.19.2
    • matplotlib>=3.4.1
    • tifffile>=2022.2.9
    • imagecodecs>=2023.3.16
    • torch>=1.11
    • monai[einops,nibabel]>=0.9.0
    • itk
    • tqdm
    • pyclesperanto-prototype
    • matplotlib