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3D-4D-Retinal-Analysis-Software

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3D/4D Retinal Analysis Software

Medical imaging software for visualizing and analyzing 3D/4D microscopy data (similar to Imaris).

Project Status

3D/4D Retinal Analysis Software

Medical imaging software for visualizing and analyzing 3D/4D microscopy data (similar to Imaris).

Project Status

✅ Phase 1 Complete: Foundation Layer (Math Module)

• Vector3, Matrix4, Ray, BoundingBox
• 100 unit tests with full coverage
• See docs/PHASE1_COMPLETE.txt for details

✅ Phase 2 Complete: Core Data Structures

• ImageVolume, Channel, TimePoint, Dataset
• 109 unit tests with full coverage
• 4D (3D + time) data management
• See docs/PHASE2_COMPLETE.txt for details

✅ Phase 3 Complete: Rendering Foundations

• Framebuffer, Camera, TransferFunction
• 78 unit tests with full coverage
• Rendering pipeline infrastructure
• See docs/PHASE3_COMPLETE.txt for details

✅ Phase 4 Complete: Volume Rendering

• RayMarcher, VolumeRenderer
• 43 unit tests with full coverage
• Ray casting, MIP rendering modes
• Multi-channel compositing
• See docs/PHASE4_COMPLETE.txt for details

✅ Phase 5 Complete: Interactive Controls

• CameraController, TimeController
• 89 unit tests with full coverage
• Mouse-based 3D navigation (arcball rotation, pan, zoom)
• Temporal navigation and animation playback
• See docs/PHASE5_COMPLETE.txt for details

✅ Phase 6 Complete: User Interface

• UIManager, TimelineWidget, ChannelPanel, ContrastPanel
• 71 unit tests with full coverage
• 4D temporal scrubbing and playback control
• Multi-channel visibility and property management
• Histogram and contrast adjustment widgets
• See docs/PHASE6_COMPLETE.txt for details

Total: 529 tests passing, ~10,000 lines of tested code

Prerequisites

macOS

1. Xcode Command Line Tools

   xcode-select --install

2. Homebrew (if not installed)

   /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

3. CMake

   brew install cmake

4. Google Test (for unit tests)

   brew install googletest

Building the Project

Quick Start

# Create build directory
mkdir build
cd build

# Configure with CMake (using Ninja)
cmake .. -G Ninja

# Build
ninja

# Run tests (if Google Test is installed)
ctest --output-on-failure

Detailed Build Steps

1. Configure the project

   mkdir -p build
   cd build
   cmake .. -G Ninja -DCMAKE_BUILD_TYPE=Release

Build all libraries**

ninja

3. Build and run tests

   ctest --output-on-failure

   Or use CTest:

   ctest --verbose

Build Options

• Build without tests: cmake .. -G Ninja -DBUILD_TESTS=OFF
• Debug build: cmake .. -G Ninja -DCMAKE_BUILD_TYPE=Debug
• Show verbose output: ninja -v

IDE Setup

Visual Studio Code

The workspace is pre-configured with:

• .vscode/c_cpp_properties.json - IntelliSense configuration
• CMake integration recommended

Recommended Extensions:

• C/C++ (Microsoft)
• CMake Tools
• CMake (twxs)

IntelliSense Issues?

1. Press Cmd+Shift+P
2. Select "C/C++: Edit Configurations (UI)"
3. Verify include paths point to your project

Project Structure

3D:4D Retinal Analysis Software/
├── src/
│   ├── math/              # Phase 1: Math utilities
│   │   ├── Vector3.h/cpp
│   │   ├── Matrix4.h/cpp
│   │   ├── Ray.h/cpp
│   │   └── BoundingBox.h/cpp
│   ├── data/              # Phase 2: Data structures
│   │   ├── ImageVolume.h/cpp
│   │   ├── Channel.h/cpp
│   │   ├── TimePoint.h/cpp
│   │   └── Dataset.h/cpp
│   ├── rendering/         # Phase 3 & 4: Rendering
│   │   ├── Framebuffer.h/cpp
│   │   ├── TransferFunction.h/cpp
│   │   ├── RayMarcher.h/cpp
│   │   └── VolumeRenderer.h/cpp
│   ├── camera/            # Phase 3 & 5: Camera system
│   │   ├── Camera.h/cpp
│   │   └── CameraController.h/cpp
│   └── animation/         # Phase 5: Temporal control
│       └── TimeController.h/cpp
├── tests/
│   ├── math/              # Phase 1 tests (100)
│   ├── data/              # Phase 2 tests (109)
│   ├── rendering/         # Phase 3 & 4 tests (92)
│   ├── camera/            # Phase 3 & 5 tests (69)
│   └── animation/         # Phase 5 tests (48)
├── docs/                  # Documentation
│   ├── PHASE1_COMPLETE.txt
│   │   ├── PHASE2_COMPLETE.txt
│   │   ├── PHASE3_COMPLETE.txt
│   │   ├── PHASE4_COMPLETE.txt
│   │   └── PHASE5_COMPLETE.txt
├── CMakeLists.txt         # Build configuration
├── architecture_design.txt # System architecture
└── 3d_4d_viewer_pseudocode.txt # Implementation guide

Development Workflow

We follow Test-Driven Development (TDD):

1. Write tests first (RED phase)
2. Implement to pass tests (GREEN phase)
3. Refactor and document (REFACTOR phase)

Running Tests

# All tests (418 tests)
cd build && ctest

# Phase 1 tests only
ctest -R "Vector3|Matrix4|Ray|BoundingBox"

# Phase 2 tests only
ctest -R "ImageVolume|Channel|TimePoint|Dataset"

# Phase 3 tests only
ctest -R "Framebuffer|Camera|TransferFunction"

# Phase 4 tests only
ctest -R "RayMarcher|VolumeRenderer"

# Phase 5 tests only
ctest -R "CameraController|TimeController"

# Specific test suite
./math_tests --gtest_filter=Vector3Test.*

# Verbose output
ctest --verbose

Troubleshooting

"cannot open source file gtest/gtest.h"

Solution: Install Google Test

brew install googletest

Then rebuild:

cd build
cmake .. -G Ninja
ninja

"Include errors detected" in VS Code

Solution 1: Reload VS Code IntelliSense

• Press Cmd+Shift+P
• Select "C/C++: Reset IntelliSense Database"

Solution 2: Check compiler path

which clang++
# Should output: /usr/bin/clang++

Update .vscode/c_cpp_properties.json if path differs.

CMake can't find Google Test

Solution: Specify Google Test location

cmake .. -DGTEST_ROOT=/opt/homebrew

Or on Intel Macs:

cmake .. -DGTEST_ROOT=/usr/local

Next Phases

• Phase 6: User Interface (Qt/ImGui, widgets, panels)
• Phase 7: Advanced Rendering (shadows, lighting, advanced transfer functions)
• Phase 8: Data Import/Export (TIFF stacks, OME-TIFF, HDF5)
• Phase 9: Analysis Tools (measurements, segmentation, tracking)
• Phase 10: Performance Optimization (GPU acceleration, streaming)

See architecture_design.txt for complete development roadmap.

Contributing

This project follows strict architecture patterns:

• Hub and Spoke design (loose coupling)
• Test-first development
• Comprehensive documentation
• Zero circular dependencies

License

[To be determined]

Contact

[To be determined]