Voxel

VoxelStack Monorepo

SPIM Software Stack Monorepo

Directory Structure

voxel/
├── python/
│   ├── core/              # python package: voxel-core
│   ├── drivers/           # python package: voxel-drivers
│   ├── web-backend/       # python package: voxel-web-backend
│   └── qt-widgets/        # python package: voxel-qt
├── js/
│   ├── svelte-widgets/    # npm package: voxel-svelte-widgets
│   └── react-widgets/     # npm package: voxel-react-widgets
│
├── microscopes/
│   ├── exaspim/
│   │   ├── backend/
│   │   └── frontend/
│   └── extreme/
│       ├── backend/
│       └── frontend/
│
├── config/                    # shared YAML schemas & examples
├── docs/                      # deeper architecture and development guides
├── examples/                  # runnable demos & templates
├── scripts/                   # tooling helpers (bootstrapping, codegen)
├── tests/                     # integration tests covering Python & JS
├── CONTRIBUTING.md            # How to get started, workspace setup, coding conventions
├── pyproject.toml             # uv workspace: `libs/python/*` and `microscopes/*/backend` (python)
├── package.json               # pnpm workspace: `libs/js/*` and `microscopes/*/frontend` (javascript)
└── README.md                  # High-level overview + quickstart

Inter Package Dependency Graph

graph LR
  subgraph libs [Libraries]
    subgraph python-libs [Python Libs]
        voxel-core --> voxel-drivers
        voxel-core --> voxel-web-backend
        voxel-core --> qt-widgets
    end

    subgraph js-widgets [JS Widgets]
        svelte-widgets
        react-widgets
    end
  end

  subgraph microscopes [Microscopes]
    subgraph exaspim [Microscope: exaspim]
      exaspim-backend --> exaspim-frontend
    end

    subgraph extreme [Microscope: extreme]
        extreme-backend --> extreme-frontend
    end
  end

  %% Dependencies: Python libs → backends
  voxel-drivers --> exaspim-backend
  voxel-drivers --> extreme-backend
  voxel-web-backend --> exaspim-backend
  voxel-web-backend --> extreme-backend

  %% Dependencies: JS Widgets → frontends
  js-widgets --> exaspim-frontend
  js-widgets --> extreme-frontend

  %% Define reusable classes
  classDef libCluster fill:#2E3440,stroke:#88C0D0,stroke-width:2px,fill-opacity:0.1;
  classDef microscopeCluster fill:#2E3440,stroke:#BF616A,stroke-width:2px,fill-opacity:0.1;
  classDef microscopeNode fill:none,stroke:#BF616A,stroke-width:1px;

  %% Apply classes
  class libs,python-libs,js-widgets libCluster;
  class microscopes microscopeCluster;
  class exaspim,extreme microscopeNode;

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Contributing

This repository uses the following branching strategy:

• main: Contains production-ready code. Updated only for releases and hotfixes.
• develop: Default branch. Contains the latest development changes.
• feature/*: Used for developing new features. Branch off from and merge back into develop.
• hotfix/*: Used for critical bug fixes. Branch off from main, and merge to both main and develop.

Contributors should typically branch off from and create pull requests to develop.

Refer to the CONTRIBUTING.md file for more details.