🦇 Bruce
A napari plugin for creating PALMRobo elements using StarDist segmentation
Description
Bruce is a napari plugin for automated detection of cells of interest in PALM RoboSoftware images, enabling fast laser capture microdissection on the PALM MicroBeam system.
Key features:
- Load 2-channel images and metadata from
.zvifiles produced by PALMRobo 4.9 - Perform StarDist-based cell segmentation (default or user-defined models)
- Allow manual editing of ROIs / elements in napari
- Perform ROI overlap analysis between 2 channels
- Export element list as
.txtfile compatible with PALMRobo 4.9
System requirements
- Conda / Mamba (recommended)
- Install Miniforge from: https://github.com/conda-forge/miniforge
- Java (OpenJDK) – required for Bio-Formats
.zvi → OME-TIFFconversion - GPU (optional) – for accelerated StarDist inference
Installation
Bruce requires a platform-specific Conda environment due to differences in native dependencies and GPU support. Predefined environment files are provided in the env/ directory:
| Platform | Environment file |
|-------------------------|--------------------------------------|
| Windows (native) | `env/bruce-env_windows_native.yml` |
| macOS (Apple Silicon) | `env/bruce-env_macos_arm.yml` |
| Linux | `env/bruce-env_linux.yml` |
Open a terminal and run:
# Create the conda environment (replace <ENV_FILE> with the appropriate .yml file)
mamba env create -f <ENV_FILE>
# Activate the environment
mamba activate bruce-env
# Install Bruce from PyPI
pip install napari-bruce
# Launch Bruce via the command line
bruce
# Or launch Bruce directly from napari
napari --with napari-bruce
# Show help
bruce -h
Configuration
Bruce stores its configuration in a user-specific JSON file.
Available commands:
# Show config file path
bruce --show-config-path
# Open config file in default text editor
bruce --open-config-file
# Edit config in a dedicated GUI window
bruce --edit-config
# Reset config to defaults
bruce --reset-config
GPU support & StarDist models
Bruce runs StarDist predictions on the GPU when visible to TensorFlow, and supports user-defined StarDist models.
Available commands:
# Check whether GPU(s) are visible to TensorFlow
bruce --gpu-status
# List available StarDist models
bruce --list-models
# Add a user-defined StarDist model located at <MODEL_DIR>
bruce --add-model <MODEL_DIR>
Image annotation for model training
Bruce comes with a dedicated GUI to annotate 2-channel images produced by PALMRobo 4.9.
Available commands:
# Construct an image set from 2-channel .zvi files located at <IN_DIR> and save to <OUT_DIR>/imgs.pkl
bruce --zvi-to-dict <IN_DIR> <OUT_DIR>
# Open the annotation GUI to label the image set at <IN_DIR>/imgs.pkl and save image/mask pairs to <OUT_DIR>/imgs_annotated.pkl
bruce --annotate <IN_DIR> <OUT_DIR>
Example images
Example .zvi files are provided in the example_images/ directory for testing and demonstration purposes.
They are not installed with the napari-bruce Python package.
1 maintainer
Metadata
1 maintainer
Release files for napari-bruce 0.6.2
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| File | Size | Uploaded | Provenance | |
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| napari_bruce-0.6.2.tar.gz | 72.8 MB | Without provenance | Details |
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| napari_bruce-0.6.2-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 145.6 MB
Release files / napari_bruce-0.6.2.tar.gz
| Download URL | napari_bruce-0.6.2.tar.gz |
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| Size | 72.8 MB |
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Release files / napari_bruce-0.6.2-py3-none-any.whl
| Download URL | napari_bruce-0.6.2-py3-none-any.whl |
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| Size | 72.8 MB |
| Tags | Python 3 |
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