Welcome to SimBA’s documentation!

These docs are under development. For detailed tutorials, code, and more extensive documentation see the SimBA GitHub repository.

For support, see SimBA Gitter channel.

Pre-print

Installation

pip install simba-uw-tf-dev

API REFERENCE:

• API Reference
  • Data processors
    • Aggregate classifier statistics calculator
    • Directing-other-animals calculator
    • Forward-spike-time-tiling coefficient calculator
    • Pose interpolator calculator
    • Pose interpolator and smoothing calculators
    • Kleinberg calculator
    • Movement calculator
    • Pup-retrieval calculator
    • SimBA pyburst calculator
    • Severity calculator
    • Classifier time-bins calculator
    • Movement time-bins calculator
    • Mutual exclusivity refactorer
    • Boolean conditional calculator
    • Gibbs sampling
    • Spontaneous alternation calculator
  • Pose estimation importers
    • Import single DLC CSV file
    • Import multiple DLC CSV files
    • Import MARS pose-estimation data
    • Import DANNCE pose-estimation data
    • Import SLEAP CSV pose-estimation data
    • Import SLEAP H5 pose-estimation data
    • Import SLEAP SLP pose-estimation data
    • Import APT TRK pose-estimation data
    • Import DLC H5 files
  • Mixins
    • Config reader methods
    • Feature extraction methods
    • Geometry transformation methods
    • Network (Graph) methods
    • Feature extraction supplement methods
    • Statistics methods
    • Circular feature extraction methods
    • Plotting methods
    • GUI pop-up methods
    • Pose importing methods
    • Modelling methods
    • Time-series feature methods
    • Unsupervised methods
    • Annotation GUI methods
    • Image attribute extraction
  • SimBA bounding-box tools (animal-anchoired ROIs)
    • Aggregate Statistics
    • GUI Tool
    • Statistics
    • Find Boundaries
    • Visualize
  • Cue light tools
    • Analyze
    • CLF Statistics
    • GUI
    • Movement statistics
    • Tools
    • Visualize
  • Feature extractors
    • Default feature extractor for 1 animals and 14 body-parts
    • Default feature extractor for 1 animals and 16 body-parts
    • Default feature extractor for 1 animals and 4 body-parts
    • Default feature extractor for 1 animals and 7 body-parts
    • Default feature extractor for 1 animals and 8 body-parts
    • Default feature extractor for 2 animals and 16 body-parts
    • Default feature extractor for 1 animals and 9 body-parts
    • Default feature extractor for user-defined body-parts
    • Feature extractor for feature subset family
    • Jitted methods for convex-hull related calculations
  • Labelling
    • Extracting labelled images
    • SimBA advanced GUI labelling interface
    • SimBA GUI labelling interface
    • Playing videos in the annotation interface
  • Outlier correction tools
    • Location outlier methods
    • Movement outlier methods
    • Advanced movement outlier correction
    • Advanced location outlier correction
    • Skipping outlier correction
  • Plotting / visualization
    • Direction between animals
    • Direction between animals - multiprocess
    • ROI feature visualization
    • ROI feature visualization - multiprocess
    • ROI visualizer
    • ROI visualizer - multiprocess
    • Circular base feature plotter
    • Circular diffusion plotting
    • Classifier validation
    • Data plotter
    • Distance plotter
    • Distance plotter - multiprocess
    • Quick path plot (Ez path plot)
    • Merge videos
    • Gantt plot
    • Gantt plot - multiprocess
    • Classifier heatmaps
    • Classifier heatmaps - multiprocess
    • Location heatmaps
    • Location heatmaps - multiprocess
    • Interactive classifier probability plotter
    • Path plotter
    • Path plotter - multiprocess
    • Classification plotter
    • Classification plotter - multiprocess
    • Pose-estimation plotter
    • Classification probability plotter
    • Classification probability plotter - multiprocess
    • SHAP aggregation plotter
    • Single video validation plotter
    • Single video validation plotter - multiprocess
    • Geometry plotter (generic)
    • Spontaneous alternation plotter
  • Pose-estimation data processors
    • Reset pose
    • Remove key-points
    • Re-organize key-points
    • Reverse pose
  • Region-of-interest tools
    • ROI analyzer
    • ROI classification calculator
    • ROI GUI
    • ROI directing analyzer
    • ROI feature analyzer
    • ROI GUI - IMAGE
    • ROI GUI
    • Moving roi shapes
    • ROI Movement analyzer
    • Multiply ROIs
    • ROI resetter
    • ROI size calculators
    • ROI size standardizer through pixels by millimeter
    • ROI time-bin calculator
    • ROI zoom methods
  • Third-party behavior labels (annotation) appenders
    • BENTO
    • BORIS
    • Deepethogram
    • Ethovison
    • Noldus Observer
    • Solomon coder
    • Generic third-party appender tool
  • SimBA UI
    • SimBA UI pop-ups
    • simba.ui.create_project_ui module
    • simba.ui.machine_model_settings_ui module
    • simba.ui.tkinter_functions module
    • simba.ui.user_defined_pose_creator module
    • simba.ui.video_info_ui module
    • Module contents
  • Unsupervised analyses in SimBA
    • Bout aggregation helper
    • Cluster frequentist statistics calculator
    • Cluster video visualizer
    • Cluster XAI calculator
    • Data extractor
    • Data creator
    • Density-based cluster validation (DBCV)
    • Embedding correlation calculator
    • Grid-search visualizer
    • HDBSCAN clusterer
    • UMAP embedder
  • SimBA utilities
    • Variable checks
    • SimBA project config creator
    • Data utilities
    • Enums
    • Errors
    • Lookups
    • Printing
    • Reading and writing
    • Warnings
  • simba.utils.cli package
    • SimBA CLI tools
  • Video processors
    • Batch process
    • Get pixels per millimeter
    • Extract frames
    • Extract .SEQ frames
    • Multi-cropper
    • Get pixels per millimeter - old
    • Video processing tools
    • Crop ROI selector (rectangles)
    • Crop ROI selector (circles)
    • Crop ROI selector (polygons)

NOTEBOOKS:

• Notebooks
  • General processing
    • Example 1: Import / Analyze
    • Shapley calculations: Example I
    • Outlier correction
    • Append third-party annotations
    • Advanced smoothing and interpolation
    • Advanced outlier correction
    • Kleinberg batch
      • This notebook iterates over a batch of Kleinberg hyperparameters on a set of input files containing behavior classifications. The results of each iteration is saved in a separate output directory. Before running the code, make sure you have simba-uw-tf-dev > 1.82.5 installed.
    • Train models I
      • TRAIN A SINGLE MODEL
      • TRAIN MULTIPLE MODELS: ONE FOR EACH SETTINGS FILE PRESENT IN THE PROJECT_FOLDER/CONFIGS DIRECTORY.
  • Visualizations
    • Create path plots in SIMBA
    • Classification validation video clips
      • Create video clips with overlaid classified events for detection of false positive event bouts
    • Gantt plots
    • Body-part distance plots
    • Classification results
    • Plot pose-estimation
    • ROI feature visualization
      • EXAMPLE 1
      • EXAMPLE 2
    • Classification probability plots
    • Location heatmap plots
    • Heatmap classification locations
  • Geometry- and image-related calculators
    • GEOMETRY MIXINS EXAMPLE I
    • GEOMETRY MIXINS EXAMPLE II
    • GEOMETRY MIXINS EXAMPLE III
      • Here we create simple images representing the animals path using geometry linestrings.
  • Miscellaneous
    • Import SLEAP H5 files
    • Multi-class classifiers
      • CREATE MULTI-CLASS CLASSIFIERS REQUIREMENTS
        • CREATE A SINGLE MULTI-CLASS CLASSIFIER
        • CREATE MULTIPLE MULTI-CLASS CLASSIFIER, ONE FOR EACH FILE INSIDE THE PROJECT_FOLDER/CONFIGS DIRECTORY
        • RUN INFERENCE
        • VISUALIZE RESULTS

USER GUIDE / TUTORIALS:

• Tutorials

WALKTHROUGHS:

• Walkthroughs

LABELLING TUTORIALS:

• Labelling

FAQ:

• Friendly Asked Questions (FAQ)

DOCS:

• SimBA basic workflow

ABOUT:

• Credits
• Who writes this stuff??
  • Notes on development
• Links