napari-bruce 0.3.0

A napari plugin for drawing PALM RoboSoftware elements using StarDist segmentation

🦇 Bruce

A napari plugin for creating PALMRobo elements using StarDist segmentation

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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 .zvi files 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 .txt file compatible with PALMRobo 4.9

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System requirements

• Conda / Mamba (recommended)
  • Install Miniforge from: https://github.com/conda-forge/miniforge
• Java (OpenJDK) – required for Bio-Formats .zvi → OME-TIFF conversion
• GPU (optional) – for accelerated StarDist inference

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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`        |

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

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Configuration

Bruce stores its configuration in a user-specific JSON file.

Available commands:

# Show config file path
bruce --show-config-path

# Open config in default editor
bruce --edit-config

# Reset config to defaults
bruce --reset-config

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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>

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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>

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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.