📚 Notebooks

A collection of examples for running SimBA through custom code — useful for batch/scripted processing and for unlocking functionality beyond the GUI.

⚙️ General processing

Run core SimBA steps from code — outlier correction, smoothing, model training, and SHAP explainability.

• Import data and perform classifications (Example 1)
• Shapley calculations: Example I (single core)
• Shapley calculations: Example II (multiple cores)
• Shapley calculations: Example III (GPU)
• Outlier correction
• Append third-party annotations
• Advanced smoothing and interpolation
• Advanced outlier correction
• Kleinberg batch / grid-search
• Train models: Example 1

📊 Visualizations

Generate plots, Gantt charts, heatmaps, paths, and annotated videos from your project data.

• Create path plots in SimBA
• Classification validation video clips
• Gantt plots
• Body-part distance plots
• Classification results
• Plot pose-estimation
• ROI feature visualization
• Classification probability plots
• Location heatmap plots
• Heatmap classification locations
• POSE ESTIMATION PLOTTING (GPU)

📐 Geometry- and image-related calculators

Treat animals and environments as geometries, plus image/video helpers (YOLO, background removal, egocentric alignment).

• Geometry computations Example 1: Movement key-point statistics in grid-system
• Geometry computations Example 2: Movement hull statistics in grid-system
• Geometry computations Example 3: Animal paths
• Geometry computations Example 4: Slice animal videos on CPU
• Geometry computations Example 5: Slice animal shapes
• Geometry computations Example 6: ROI and path statistics
• Geometry computations: Example 7
• YOLO bounding boxes: Example 1
• Remove video background
• Egocentric data and video alignment
• Blob tracking with SimBA
• 📹 Blob tracking visualization

🧰 Miscellaneous

Data import, multi-class classifiers, and ROI-definition helpers.

• Import SLEAP H5 files
• Multi-class classifiers
• Manually define ROIs