Installation¶
Requirements¶
- Python 3.14+
- Operating System: macOS, Windows, or Linux
Install from Source¶
git clone https://github.com/m00zu/Synapse
cd Synapse
pip install .
Launch:
synapse
Or with a virtual environment (recommended):
conda create -n synapse python=3.14
conda activate synapse
pip install .
synapse
Optional: Rust-accelerated Modules¶
Synapse works fully with pure Python, but optional Rust extensions provide significant speedups for OIR microscopy file reading and image processing:
# Install Rust toolchain (one time)
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
# Build OIR reader
cd oir_reader_rs && maturin develop --release && cd ..
# Build image processing
cd image_process_rs && maturin develop --release && cd ..
Installing Plugins¶
Synapse ships with core data processing nodes. Image analysis, statistics, plotting, and other domain-specific nodes are available as plugins.
Method 1: In-app (recommended)¶
- Go to Plugins > Install Plugin in the menu bar
- Select a
.py,.zip, or.synpkgfile - Click Plugins > Reload Plugins — new nodes appear in the Node Explorer
Method 2: Manual¶
Drop plugin files directly into the plugins/ directory:
| Platform | Plugin directory |
|---|---|
| macOS | ~/Library/Application Support/Synapse/plugins/ |
| Windows | %APPDATA%\Synapse\plugins\ |
| Linux | ~/.config/Synapse/plugins/ |
| From source | ./plugins/ (next to synapse/) |
Available Plugins¶
| Plugin | Description |
|---|---|
| Image Analysis | Filters, thresholding, morphology, segmentation, measurements, ROI |
| Statistical Analysis | t-tests, ANOVA, regression, survival analysis, PCA |
| Figure Plotting | Scatter, box, violin, heatmap, volcano, regression plots |
| SAM2 Segmentation | Interactive click-to-segment, multi-object, auto-segment |
| Cellpose | Cell/nucleus segmentation (ONNX, no PyTorch) |
| Video & Tracking | Frame extraction, object tracking, trajectory analysis |
| 3D Volume | Volume rendering and analysis |
| Cheminformatics | Molecule editing, docking, protein prep |
| Filopodia | Cell protrusion detection and measurement |
All plugin dependencies are bundled or auto-downloaded on first use. No manual pip install required.
Verifying Installation¶
After launching, you should see:
- The node canvas (center) — where you build pipelines
- The Node Explorer (left) — browse and search for nodes
- The Properties panel (right) — configure the selected node
Press Ctrl+F to search for nodes, or right-click on the canvas to browse the node menu.