{"name":"napari-bruce","display_name":"napari-bruce","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-bruce.run","title":"Bruce","python_name":"napari_bruce.main_widget:PluginManager","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-bruce.run","display_name":"Bruce","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-bruce","version":"0.2.4","dynamic":null,"platform":null,"supported_platform":null,"summary":"A napari plugin for drawing PALM RoboSoftware elements using StarDist segmentation","description":"# ***🦇 Bruce***\n\n**A napari plugin for creating PALMRobo elements using StarDist segmentation**\n\n\n---\n\n## Description\n\n**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.\n\nKey features:\n- Load 2-channel images and metadata from `.zvi` files produced by PALMRobo 4.9\n- Perform StarDist-based cell segmentation (default or user-defined models)\n- Allow manual editing of ROIs / elements in napari\n- Perform ROI overlap analysis between 2 channels\n- Export element list as `.txt` file compatible with PALMRobo 4.9\n\n\n---\n\n\n## System requirements\n\n- **Conda / Mamba** (recommended)\n  - Install Miniforge from: https://github.com/conda-forge/miniforge\n- **Java (OpenJDK)** – required for Bio-Formats `.zvi → OME-TIFF` conversion\n- **GPU (optional)** – for accelerated StarDist inference\n\n\n---\n\n\n## Installation\n\nBruce requires a **platform-specific Conda environment** due to differences in native dependencies and GPU support. Predefined environment files are provided in the `env/` directory:\n\n```md\n| Platform                | Environment file                     |\n|-------------------------|--------------------------------------|\n| Windows (native)        | `env/bruce-env_windows_native.yml`   |\n| macOS (Apple Silicon)   | `env/bruce-env_macos_arm.yml`        |\n| Linux                   | `env/bruce-env_linux.yml`            |\n```\n\nOpen a terminal and run:\n\n```bash\n# Create the conda environment (replace <ENV_FILE> with the appropriate .yml file)\nmamba env create -f <ENV_FILE>\n\n# Activate the environment\nmamba activate bruce-env\n\n# Install Bruce from PyPI\npip install napari-bruce\n\n# Launch Bruce via the command line\nbruce\n\n# Or launch Bruce directly from napari\nnapari --with napari-bruce\n```\n\n\n---\n\n\n## Configuration\n\nBruce stores its configuration in a user-specific JSON file.\n\nUseful commands:\n\n```bash\n# Show config file path\nbruce --show-config-path\n\n# Open config in default editor\nbruce --edit-config\n\n# Reset config to defaults\nbruce --reset-config\n```\n\n\n---\n\n\n## GPU support & StarDist models \n\nBruce runs StarDist predictions on the GPU when visible to TensorFlow, and supports user-defined StarDist models.\n\nUseful commands:\n\n```bash\n# Check whether GPU(s) are visible to TensorFlow\nbruce --gpu-status\n\n# List available StarDist models\nbruce --list-models\n\n# Add a user-defined StarDist model (replace <MODEL_DIR> with the model directory)\nbruce --add-model <MODEL_DIR>\n```\n\n\n---\n\n\n## Example images\n\nExample `.zvi` files are provided in the `example_images/` directory for testing and demonstration purposes.\nThey are not installed with the napari-bruce Python package.\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Benjamin Vallin <ben.vallin@gmail.com>","maintainer":null,"maintainer_email":null,"license":"MIT","classifier":["Framework :: napari","Programming Language :: Python :: 3","Programming Language :: Python :: 3.10","Operating System :: OS Independent","License :: OSI Approved :: MIT License","Intended Audience :: Science/Research"],"requires_dist":["napari","PyQt5","qtpy","numpy==1.26.4","opencv-python-headless","ome-types","tifffile","pandas","matplotlib","csbdeep","stardist"],"requires_python":">=3.9","requires_external":null,"project_url":null,"provides_extra":null,"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}