📖 API Reference

This section provides a categorized reference of SimBA’s modules and methods, grouped by their functionality such as feature extraction, plotting, transformation, and modeling.

🔍 Blob tracking tools

Track animals in videos using background subtraction and blob detection. Extract geometric features (center, nose, tail, left/right points) from detected blob shapes without requiring pose-estimation data.

• SimBA Blob Tracking Methods
  • Main Executor
    • BlobTrackingExecutor
  • User Interfaces
    • BlobTrackingUI
      • BlobTrackingUI.get_roi_definitions()
    • BlobQuickChecker
  • Blob Detection Functions
    • get_blob_vertices_from_video()
    • get_nose_tail_from_vertices()
    • get_left_right_points()
    • stabilize_body_parts()
  • Background Subtraction: CPU Multiprocessing
    • video_bg_subtraction_mp()
  • Background Subtraction: GPU (CuPy)
    • bg_subtraction_cupy()
  • Background Subtraction: GPU (CUDA)
    • bg_subtraction_cuda()
  • Compute Average Frame
    • CPU-based average frame computation
      • create_average_frm()
    • GPU-based average frame computation (CuPy)
      • create_average_frm_cupy()
    • GPU-based average frame computation (CUDA)
      • create_average_frm_cuda()
  • Data Import
    • SimBABlobImporter
  • Visualization
    • BlobPlotter
    • BlobVisualizer
    • GeometryPlotter

📦 Bounding-box tools

Detect animal interactions via overlapping bounding boxes.

See tutorial: Cue-light tutorial

• Aggregate Statistics
  • AggBoundaryStatisticsCalculator
• GUI Tool
  • BoundaryMenus
• Statistics
  • BoundaryStatisticsCalculator
• Find Boundaries
  • AnimalBoundaryFinder
• Visualize
  • BoundaryVisualizer
• YOLO methods
  • Utilities
  • Bounding-box inference
  • NVDEC GPU-accelerated YOLO inference
  • Pose-estimation inference
  • YOLO pose-estimation segmentation visualizer
  • YOLO pose-estimation segmentation inference
  • Pose-estimation track inference
  • Pose-estimation track plotting
  • Pose-estimation plotting
  • Bounding box plotting
  • YOLO annotation visualizer
  • COCO key-points -> YOLO pose-estimation format conversion
  • COCO key-points -> YOLO bounding box conversion
  • COCO key-points -> YOLO segmentation conversion
  • SAM3 -> YOLO segmentation project
  • SAM3 -> YOLO bounding-box (detection) project
  • Merge multiple YOLO projects
  • Multi-animal DeepLabCut predictions -> YOLO pose-estimation annotations format conversion
  • DeepLabCut predictions -> YOLO pose-estimation annotations
  • Labelme annotations -> YOLO bounding box annotations
  • Labelme points -> YOLO keypoints annotations
  • Labelme points -> YOLO segmentation annotations
  • SimBA ROIs -> YOLO bounding box annotations
  • SimBA pose-estimation -> YOLO pose-estimation annotations
  • SimBA pose-estimation -> YOLO segmentation annotations
  • SLEAP CSV predictions -> YOLO pose-estimation annotations
  • SLEAP H5 predictions -> YOLO pose-estimation annotations
  • SLEAP annotations -> YOLO pose-estimation annotations
  • LightningPose keypoints -> YOLO bounding box conversion
  • LightningPose keypoints -> YOLO pose-estimation annotations

🔁 Circular transformations

Statistical operations for circular data like head direction. Wraparound-aware, multi-animal capable, and based on body-part derived base angles.

• Circular statistics mixin
  • CircularStatisticsMixin
    • CircularStatisticsMixin.agg_angular_diff_timebins()
    • CircularStatisticsMixin.circular_correlation()
    • CircularStatisticsMixin.circular_hotspots()
    • CircularStatisticsMixin.circular_mean()
    • CircularStatisticsMixin.circular_range()
    • CircularStatisticsMixin.circular_std()
    • CircularStatisticsMixin.degrees_to_cardinal()
    • CircularStatisticsMixin.direction_three_bps()
    • CircularStatisticsMixin.direction_two_bps()
    • CircularStatisticsMixin.fit_circle()
    • CircularStatisticsMixin.hodges_ajne()
    • CircularStatisticsMixin.instantaneous_angular_velocity()
    • CircularStatisticsMixin.kuipers_two_sample_test()
    • CircularStatisticsMixin.mean_resultant_vector_length()
    • CircularStatisticsMixin.preferred_turning_direction()
    • CircularStatisticsMixin.rao_spacing()
    • CircularStatisticsMixin.rayleigh()
    • CircularStatisticsMixin.rotational_direction()
    • CircularStatisticsMixin.sliding_angular_diff()
    • CircularStatisticsMixin.sliding_bearing()
    • CircularStatisticsMixin.sliding_circular_correlation()
    • CircularStatisticsMixin.sliding_circular_hotspots()
    • CircularStatisticsMixin.sliding_circular_mean()
    • CircularStatisticsMixin.sliding_circular_range()
    • CircularStatisticsMixin.sliding_circular_std()
    • CircularStatisticsMixin.sliding_hodges_ajne()
    • CircularStatisticsMixin.sliding_kuipers_two_sample_test()
    • CircularStatisticsMixin.sliding_mean_resultant_vector_length()
    • CircularStatisticsMixin.sliding_preferred_turning_direction()
    • CircularStatisticsMixin.sliding_rao_spacing()
    • CircularStatisticsMixin.sliding_rayleigh_z()
    • CircularStatisticsMixin.three_point_direction()
    • CircularStatisticsMixin.two_point_direction()
    • CircularStatisticsMixin.watson_williams_test()
    • CircularStatisticsMixin.watsons_u()
• Circular GPU methods
  • direction_from_three_bps()
  • direction_from_two_bps()
  • instantaneous_angular_velocity()
  • rotational_direction()
  • sliding_angular_diff()
  • sliding_bearing()
  • sliding_circular_hotspots()
  • sliding_circular_mean()
  • sliding_circular_range()
  • sliding_circular_std()
  • sliding_rayleigh_z()
  • sliding_resultant_vector_length()

🔧 Config reader

Parse SimBA config files and access project-specific metadata.

• Config reader
  • ConfigReader

💡 Cue-light tools

Link animal behavior to cue-light on/off states.

See tutorial: Cue-light tutorial

• Cue light analyzer
  • CueLightAnalyzer
• Cue light classification statistics
  • CueLightClfAnalyzer
• Cue light movement statistics
  • CueLightMovementAnalyzer
• Cue light plotting
  • CueLightVisualizer

🔧 Data processing tools

Transform classification, tracking, and image data.

• Aggregate classifier statistics calculator
• Interpolate pose-estimation data
• Advanced pose-estimation interpolation
• Smooth pose-estimation data
• Advanced smooth pose-estimation data
• Directing-other-animals calculator
• Directing-other-animals body-parts 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
• Movement time-bins calculator (multiprocess)
• Aggregate classifier statistics (multiprocess)
• Directing-animal-to-bodypart calculator
• Severity bout-based calculator
• Severity frame-based calculator
• YOLO track cleaner
• SHAP log (GPU)
• Mutual exclusivity refactorer
• Boolean conditional calculator
• Gibbs sampling
• Spontaneous alternation calculator
• “Blob” location detector
• Egocentric data / video alignment
• Heuristic circling detector
• Heuristic freezing detector
• Data GPU methods
• Light-dark box analysis

📏 Feature extraction mixins

Core low-level feature methods used in SimBA’s default extraction pipelines.

• Feature extraction methods
  • FeatureExtractionMixin
    • FeatureExtractionMixin.angle3pt()
    • FeatureExtractionMixin.angle3pt_vectorized()
    • FeatureExtractionMixin.bodypart_distance()
    • FeatureExtractionMixin.cdist()
    • FeatureExtractionMixin.cdist_3d()
    • FeatureExtractionMixin.change_in_bodypart_euclidean_distance()
    • FeatureExtractionMixin.check_directionality_cords()
    • FeatureExtractionMixin.check_directionality_viable()
    • FeatureExtractionMixin.convex_hull_calculator_mp()
    • FeatureExtractionMixin.cosine_similarity()
    • FeatureExtractionMixin.count_values_in_range()
    • FeatureExtractionMixin.create_shifted_array()
    • FeatureExtractionMixin.create_shifted_df()
    • FeatureExtractionMixin.dataframe_gaussian_smoother()
    • FeatureExtractionMixin.dataframe_savgol_smoother()
    • FeatureExtractionMixin.euclidean_distance()
    • FeatureExtractionMixin.find_midpoints()
    • FeatureExtractionMixin.framewise_bodypart_movement()
    • FeatureExtractionMixin.framewise_euclidean_distance()
    • FeatureExtractionMixin.framewise_euclidean_distance_roi()
    • FeatureExtractionMixin.framewise_inside_polygon_roi()
    • FeatureExtractionMixin.framewise_inside_rectangle_roi()
    • FeatureExtractionMixin.get_bp_headers()
    • FeatureExtractionMixin.get_feature_extraction_headers()
    • FeatureExtractionMixin.insert_default_headers_for_feature_extraction()
    • FeatureExtractionMixin.is_inside_circle()
    • FeatureExtractionMixin.jitted_line_crosses_to_nonstatic_targets()
    • FeatureExtractionMixin.jitted_line_crosses_to_static_targets()
    • FeatureExtractionMixin.keypoint_distances()
    • FeatureExtractionMixin.line_crosses_to_static_targets()
    • FeatureExtractionMixin.minimum_bounding_rectangle()
    • FeatureExtractionMixin.three_point_angle()
    • FeatureExtractionMixin.windowed_frequentist_distribution_tests()
• Supplementary feature extraction methods
  • FeatureExtractionSupplemental
    • FeatureExtractionSupplemental.angle3pt()
    • FeatureExtractionSupplemental.angle3pt_vectorized()
    • FeatureExtractionSupplemental.bodypart_distance()
    • FeatureExtractionSupplemental.border_distances()
    • FeatureExtractionSupplemental.cdist()
    • FeatureExtractionSupplemental.cdist_3d()
    • FeatureExtractionSupplemental.change_in_bodypart_euclidean_distance()
    • FeatureExtractionSupplemental.check_directionality_cords()
    • FeatureExtractionSupplemental.check_directionality_viable()
    • FeatureExtractionSupplemental.consecutive_time_series_categories_count()
    • FeatureExtractionSupplemental.convex_hull_calculator_mp()
    • FeatureExtractionSupplemental.cosine_similarity()
    • FeatureExtractionSupplemental.count_values_in_range()
    • FeatureExtractionSupplemental.create_shifted_array()
    • FeatureExtractionSupplemental.create_shifted_df()
    • FeatureExtractionSupplemental.dataframe_gaussian_smoother()
    • FeatureExtractionSupplemental.dataframe_savgol_smoother()
    • FeatureExtractionSupplemental.distance_and_velocity()
    • FeatureExtractionSupplemental.euclidean_distance()
    • FeatureExtractionSupplemental.euclidean_distance_timeseries_change()
    • FeatureExtractionSupplemental.find_midpoints()
    • FeatureExtractionSupplemental.find_path_loops()
    • FeatureExtractionSupplemental.framewise_bodypart_movement()
    • FeatureExtractionSupplemental.framewise_euclidean_distance()
    • FeatureExtractionSupplemental.framewise_euclidean_distance_roi()
    • FeatureExtractionSupplemental.framewise_inside_polygon_roi()
    • FeatureExtractionSupplemental.framewise_inside_rectangle_roi()
    • FeatureExtractionSupplemental.get_bp_headers()
    • FeatureExtractionSupplemental.get_feature_extraction_headers()
    • FeatureExtractionSupplemental.img_edge_distances()
    • FeatureExtractionSupplemental.insert_default_headers_for_feature_extraction()
    • FeatureExtractionSupplemental.is_inside_circle()
    • FeatureExtractionSupplemental.jitted_line_crosses_to_nonstatic_targets()
    • FeatureExtractionSupplemental.jitted_line_crosses_to_static_targets()
    • FeatureExtractionSupplemental.keypoint_distances()
    • FeatureExtractionSupplemental.line_crosses_to_static_targets()
    • FeatureExtractionSupplemental.minimum_bounding_rectangle()
    • FeatureExtractionSupplemental.movement_stats_from_bouts_df()
    • FeatureExtractionSupplemental.peak_ratio()
    • FeatureExtractionSupplemental.rolling_categorical_switches_ratio()
    • FeatureExtractionSupplemental.rolling_horizontal_vs_vertical_movement()
    • FeatureExtractionSupplemental.rolling_peak_count_ratio()
    • FeatureExtractionSupplemental.sequential_lag_analysis()
    • FeatureExtractionSupplemental.spontaneous_alternations()
    • FeatureExtractionSupplemental.three_point_angle()
    • FeatureExtractionSupplemental.velocity_aggregator()
    • FeatureExtractionSupplemental.windowed_frequentist_distribution_tests()

📝 Feature extraction wrappers

Pre-configured “out-of-the-box” feature extraction modules for common pose-estimation schemas.

• Default feature extractor for 2 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
• Rearing and grooming feature extraction wrapper
• Straub tail feature extraction wrapper
• Mexican cave fish feature extraction wrapper
• Rat social behavior feature extraction wrapper
• Gerbil single body-part feature extraction wrapper
• Aggression feature extractor (11/25)
• AMBER pipeline feature extractor
• Boundary rearing feature extractor
• Riptortus pedestris feature extractor
• Custom feature extractor

📐 Geometry transformations

Transform pose-estimated body-part coordinates into geometric shapes (bounding boxes, polygons, circles), and compute spatial relationships like distance and intersection.

• Geometry mixin
  • GeometryMixin
    • GeometryMixin.adjust_geometry_locations()
    • GeometryMixin.area()
    • GeometryMixin.bodyparts_to_circle()
    • GeometryMixin.bodyparts_to_line()
    • GeometryMixin.bodyparts_to_multistring_skeleton()
    • GeometryMixin.bodyparts_to_points()
    • GeometryMixin.bodyparts_to_polygon()
    • GeometryMixin.bucket_img_into_grid_hexagon()
    • GeometryMixin.bucket_img_into_grid_points()
    • GeometryMixin.bucket_img_into_grid_square()
    • GeometryMixin.buffer_shape()
    • GeometryMixin.compute_pct_shape_overlap()
    • GeometryMixin.compute_shape_overlap()
    • GeometryMixin.contours_to_geometries()
    • GeometryMixin.crosses()
    • GeometryMixin.cumsum_animal_geometries_grid()
    • GeometryMixin.cumsum_bool_geometries()
    • GeometryMixin.cumsum_coord_geometries()
    • GeometryMixin.delaunay_triangulate_keypoints()
    • GeometryMixin.difference()
    • GeometryMixin.extend_line_to_bounding_box_edges()
    • GeometryMixin.filter_low_p_bps_for_shapes()
    • GeometryMixin.geometries_to_exterior_keypoints()
    • GeometryMixin.geometry_contourcomparison()
    • GeometryMixin.geometry_histocomparison()
    • GeometryMixin.geometry_transition_probabilities()
    • GeometryMixin.geometry_video()
    • GeometryMixin.get_center()
    • GeometryMixin.get_geometry_brightness_intensity()
    • GeometryMixin.get_shape_statistics()
    • GeometryMixin.hausdorff_distance()
    • GeometryMixin.is_containing()
    • GeometryMixin.is_shape_covered()
    • GeometryMixin.is_touching()
    • GeometryMixin.keypoints_to_axis_aligned_bounding_box()
    • GeometryMixin.length()
    • GeometryMixin.line_split_bounding_box()
    • GeometryMixin.linear_frechet_distance()
    • GeometryMixin.locate_line_point()
    • GeometryMixin.minimum_rotated_rectangle()
    • GeometryMixin.multiframe_area()
    • GeometryMixin.multiframe_bodypart_to_point()
    • GeometryMixin.multiframe_bodyparts_to_circle()
    • GeometryMixin.multiframe_bodyparts_to_line()
    • GeometryMixin.multiframe_bodyparts_to_multistring_skeleton()
    • GeometryMixin.multiframe_bodyparts_to_polygon()
    • GeometryMixin.multiframe_buffer_shapes()
    • GeometryMixin.multiframe_compute_pct_shape_overlap()
    • GeometryMixin.multiframe_compute_shape_overlap()
    • GeometryMixin.multiframe_delaunay_triangulate_keypoints()
    • GeometryMixin.multiframe_difference()
    • GeometryMixin.multiframe_hausdorff_distance()
    • GeometryMixin.multiframe_is_shape_covered()
    • GeometryMixin.multiframe_length()
    • GeometryMixin.multiframe_minimum_rotated_rectangle()
    • GeometryMixin.multiframe_shape_distance()
    • GeometryMixin.multiframe_symmetric_difference()
    • GeometryMixin.multiframe_union()
    • GeometryMixin.multifrm_geometry_histocomparison()
    • GeometryMixin.parallel_offset_polygon()
    • GeometryMixin.point_lineside()
    • GeometryMixin.points_in_polygon()
    • GeometryMixin.rank_shapes()
    • GeometryMixin.shape_distance()
    • GeometryMixin.simba_roi_to_geometries()
    • GeometryMixin.sleap_csv_to_geometries()
    • GeometryMixin.smooth_geometry_bspline()
    • GeometryMixin.static_point_lineside()
    • GeometryMixin.symmetric_difference()
    • GeometryMixin.to_linestring()
    • GeometryMixin.union()
    • GeometryMixin.view_shapes()
• Geometry GPU methods
  • directionality_to_nonstatic_target()
  • directionality_to_static_targets()
  • find_midpoints()
  • get_convex_hull()
  • is_inside_circle()
  • is_inside_polygon()
  • is_inside_rectangle()
  • poly_area()

🖼️ Image transformations

Slice frames and extract visual information from tracking data; compare image features across time.

• Image mixin
  • ImageMixin
    • ImageMixin.add_img_border_and_flood_fill()
    • ImageMixin.brightness_intensity()
    • ImageMixin.canny_edge_detection()
    • ImageMixin.close()
    • ImageMixin.create_time_ruler()
    • ImageMixin.create_uniform_img()
    • ImageMixin.cross_correlation_matrix()
    • ImageMixin.cross_correlation_similarity()
    • ImageMixin.erode()
    • ImageMixin.find_contours()
    • ImageMixin.find_first_non_uniform_clr_frm()
    • ImageMixin.gaussian_blur()
    • ImageMixin.get_contourmatch()
    • ImageMixin.get_histocomparison()
    • ImageMixin.get_timelapse_img()
    • ImageMixin.img_diff()
    • ImageMixin.img_emd()
    • ImageMixin.img_matrix_mse()
    • ImageMixin.img_moments()
    • ImageMixin.img_sliding_mse()
    • ImageMixin.img_stack_mse()
    • ImageMixin.img_stack_to_bw()
    • ImageMixin.img_stack_to_greyscale()
    • ImageMixin.img_stack_to_video()
    • ImageMixin.img_to_bw()
    • ImageMixin.img_to_greyscale()
    • ImageMixin.is_video_color()
    • ImageMixin.non_local_mean_denoising_image()
    • ImageMixin.non_local_mean_denoising_sequence()
    • ImageMixin.orb_matching_similarity_()
    • ImageMixin.pad_img_stack()
    • ImageMixin.read_all_img_in_dir()
    • ImageMixin.read_img_batch_from_video()
    • ImageMixin.resize_img_dict()
    • ImageMixin.resize_img_stack()
    • ImageMixin.segment_img_horizontal()
    • ImageMixin.segment_img_stack_horizontal()
    • ImageMixin.segment_img_vertical()
    • ImageMixin.slice_shapes_in_img()
    • ImageMixin.slice_shapes_in_imgs()
    • ImageMixin.sliding_cross_correlation_similarity()
    • ImageMixin.sliding_structural_similarity_index()
    • ImageMixin.structural_similarity_index()
    • ImageMixin.structural_similarity_matrix()
    • ImageMixin.template_matching_cpu()
    • ImageMixin.template_matching_gpu()
• Image GPU methods
  • average_3d_stack_cupy()
  • bg_subtraction_cuda()
  • bg_subtraction_cupy()
  • create_average_frm_cuda()
  • create_average_frm_cupy()
  • img_stack_brightness()
  • img_stack_to_bw()
  • img_stack_to_grayscale_cuda()
  • img_stack_to_grayscale_cupy()
  • pose_plotter()
  • rotate_img_stack_cupy()
  • rotate_video_cupy()
  • segment_img_stack_horizontal()
  • segment_img_stack_vertical()
  • slice_imgs()
  • sliding_psnr()
  • stack_sliding_mse()

🏷️ Labeling tools

SimBA tools for annotating behavioral events.

• Extracting labelled images
  • AnnotationFrameExtractor
• Calculate annotation statistics in SimBA project
  • AnnotationMetaDataExtractor
• SimBA advanced GUI labelling interface
  • AdvancedLabellingInterface
• SimBA GUI labelling interface
• Playing videos in the annotation interface
  • annotation_video_player()
• Annotation GUI mixins
  • AnnotatorMixin

🤖 Model tools

Create, train, and manage behavior classifiers in SimBA.

• Model mixin
  • TrainModelMixin
    • TrainModelMixin.bout_train_test_splitter()
    • TrainModelMixin.calc_learning_curve()
    • TrainModelMixin.calc_permutation_importance()
    • TrainModelMixin.calc_pr_curve()
    • TrainModelMixin.check_df_dataset_integrity()
    • TrainModelMixin.check_raw_dataset_integrity()
    • TrainModelMixin.check_sampled_dataset_integrity()
    • TrainModelMixin.check_validity_of_meta_files()
    • TrainModelMixin.clf_define()
    • TrainModelMixin.clf_fit()
    • TrainModelMixin.clf_predict_proba()
    • TrainModelMixin.create_clf_report()
    • TrainModelMixin.create_example_dt()
    • TrainModelMixin.create_meta_data_csv_training_multiple_models()
    • TrainModelMixin.create_meta_data_csv_training_one_model()
    • TrainModelMixin.create_shap_log()
    • TrainModelMixin.create_shap_log_concurrent_mp()
    • TrainModelMixin.create_shap_log_mp()
    • TrainModelMixin.create_x_importance_bar_chart()
    • TrainModelMixin.create_x_importance_log()
    • TrainModelMixin.cuml_rf_x_importances()
    • TrainModelMixin.define_scaler()
    • TrainModelMixin.define_tree_explainer()
    • TrainModelMixin.delete_other_annotation_columns()
    • TrainModelMixin.dviz_classification_visualization()
    • TrainModelMixin.find_collinear_features()
    • TrainModelMixin.find_highly_correlated_fields()
    • TrainModelMixin.find_low_variance_fields()
    • TrainModelMixin.fit_scaler()
    • TrainModelMixin.get_all_clf_names()
    • TrainModelMixin.get_model_info()
    • TrainModelMixin.insert_column_headers_for_outlier_correction()
    • TrainModelMixin.partial_dependence_calculator()
    • TrainModelMixin.print_machine_model_information()
    • TrainModelMixin.random_multiclass_bout_sampler()
    • TrainModelMixin.random_multiclass_frm_sampler()
    • TrainModelMixin.random_undersampler()
    • TrainModelMixin.read_all_files_in_folder()
    • TrainModelMixin.read_all_files_in_folder_mp()
    • TrainModelMixin.read_all_files_in_folder_mp_futures()
    • TrainModelMixin.read_in_all_model_names_to_remove()
    • TrainModelMixin.read_model_settings_from_config()
    • TrainModelMixin.read_pickle()
    • TrainModelMixin.save_rf_model()
    • TrainModelMixin.scaler_inverse_transform()
    • TrainModelMixin.scaler_transform()
    • TrainModelMixin.smote_oversampler()
    • TrainModelMixin.smoteen_oversampler()
    • TrainModelMixin.split_and_group_df()
    • TrainModelMixin.split_df_to_x_y()
• Batch random forest inference
  • InferenceBatch
    • InferenceBatch.run()
• Batch multi-animal random forest inference
  • InferenceMultiAnimalBatch
    • InferenceMultiAnimalBatch.run()
• Batch multi-class random forest inference
  • InferenceMulticlassBatch
    • InferenceMulticlassBatch.run()
• Grid-search random forest classifiers
  • GridSearchRandomForestClassifier
    • GridSearchRandomForestClassifier.perform_sampling()
    • GridSearchRandomForestClassifier.run()
• Grid-search random forest multi-classifiers
  • GridSearchMulticlassRandomForestClassifier
    • GridSearchMulticlassRandomForestClassifier.perform_sampling()
    • GridSearchMulticlassRandomForestClassifier.run()
• Random forest inference - validation
  • InferenceValidation
• Fit random forest classifier
  • TrainRandomForestClassifier
    • TrainRandomForestClassifier.perform_sampling()
    • TrainRandomForestClassifier.run()
    • TrainRandomForestClassifier.save()
• Fit random forest classifier - multi-class
  • TrainMultiClassRandomForestClassifier
    • TrainMultiClassRandomForestClassifier.run()
    • TrainMultiClassRandomForestClassifier.save_model()
• Ordinal classifier methods
  • OrdinalClassifier
    • OrdinalClassifier.fit()
    • OrdinalClassifier.load()
    • OrdinalClassifier.predict()
    • OrdinalClassifier.predict_proba()
    • OrdinalClassifier.save()
• Regression - metrics
  • mean_absolute_error()
  • mean_absolute_percentage_error()
  • mean_squared_error()
  • r2_score()
  • root_mean_squared_error()
• Regression - fit and transform
  • evaluate_xgb()
  • fit_xgb()
  • transform_xgb()
  • xgb_define()
• SAM2 segmentation inference
  • SamInference
    • SamInference.run()
• Fit YOLO model
  • FitYolo
    • FitYolo.run()
• YOLO bounding-box inference
  • YoloInference
    • YoloInference.run()

🔗 Network transformations

Build and analyze graphs derived from pose-estimation time-series data.

• Network (Graph) methods
  • NetworkMixin
    • NetworkMixin.berger_parker()
    • NetworkMixin.brillouins_index()
    • NetworkMixin.create_graph()
    • NetworkMixin.create_multigraph()
    • NetworkMixin.girvan_newman()
    • NetworkMixin.graph_current_flow_closeness_centrality()
    • NetworkMixin.graph_katz_centrality()
    • NetworkMixin.graph_page_rank()
    • NetworkMixin.margalef_diversification_index()
    • NetworkMixin.menhinicks_index()
    • NetworkMixin.multigraph_page_rank()
    • NetworkMixin.shannon_diversity_index()
    • NetworkMixin.simpson_index()
    • NetworkMixin.sorensen_dice_coefficient()
    • NetworkMixin.visualize()

⚠️ Outlier correction

Heuristic-based filtering of body-part tracking outliers.

• Location outlier removed
• Movement outlier remover
• Movement outlier remover: multi-core
• Location outlier remover: multi-core
• Advanced movement outlier correction
• Advanced location outlier correction
• Skipping outlier correction

🎨 Plotting and visualization tools

Visualize behavioral data and pose-tracking outputs.

• Direction between animals
• Direction between animals - multiprocess
• ROI feature visualization
• ROI feature visualization - multiprocess
• ROI directing visualization
  • DirectingROIVisualizer
• ROI visualizer
• ROI visualizer - multiprocess
• Circular base feature plotter
• Circular diffusion plotting
• Classifier validation
• Classifier validation - multiprocess
• Data plotter
• Distance plotter
• Distance plotter - multiprocess
• Quick path plot (Ez path plot)
• Merge videos
• Gantt plot
• Gantt plot - multiprocess
• Gantt plot - fancy
• Classifier heatmaps
• Classifier heatmaps - multiprocess
• Location heatmaps
• Location heatmaps - multiprocess
• Interactive classifier probability plotter
• Path plotter
• Path plotter - multiprocess
• Classification plotter
• Classification plotter - multiprocess
• Annotation bout plotter
• Pose-estimation plotter
• Skeleton video creator
  • SkeletonVideoCreator
    • SkeletonVideoCreator.run()
• Classification probability plotter
• Classification probability plotter - multiprocess
• SHAP aggregation plotter
• Single video validation plotter
• Single video validation plotter - multiprocess
• Geometry plotter (generic)
  • GeometryPlotter
• Spontaneous alternation plotter
• “Blob” plotter
• “Blob” plotter
• YOLO bounding-box plotter
  • YOLOVisualizer
• YOLO model comparator
  • YoloModelComparator
• Plotting methods
  • PlottingMixin
    • PlottingMixin.categorical_scatter()
    • PlottingMixin.continuous_scatter()
    • PlottingMixin.create_gantt_img()
    • PlottingMixin.create_single_color_lst()
    • PlottingMixin.draw_lines_on_img()
    • PlottingMixin.get_bouts_for_gantt()
    • PlottingMixin.get_optimal_circle_size()
    • PlottingMixin.get_optimal_font_scales()
    • PlottingMixin.get_path_img()
    • PlottingMixin.insert_directing_line()
    • PlottingMixin.joint_plot()
    • PlottingMixin.line_plot()
    • PlottingMixin.make_distance_plot()
    • PlottingMixin.make_gantt_plot()
    • PlottingMixin.make_line_plot()
    • PlottingMixin.make_line_plot_plotly()
    • PlottingMixin.make_path_plot()
    • PlottingMixin.make_probability_plot()
    • PlottingMixin.plot_bar_chart()
    • PlottingMixin.plot_clf_cumcount()
    • PlottingMixin.put_text()
    • PlottingMixin.remove_a_folder()
    • PlottingMixin.resize_gantt()
    • PlottingMixin.rotate_img()
    • PlottingMixin.split_and_group_df()
• Light-/Dark-box plotting

📦 Pose-estimation import tools

Parse, load, and process pose-estimation data from common formats.

• 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
• Reset pose
• Remove key-points
• Re-organize key-points
• Reverse pose
• Pose import mixins
• Import SimBA blob tracking as pose
• Import FaceMap body-part tracking
• Import SuperAnimal-TopView Mouse body-part tracking
• Import YOLO pose-estimation tracking (unique individuals, non-track based, only)

🗺️ ROI tools

Define and analyze regions-of-interest (ROIs) in relation to tracking data.

• ROI Analysis Tools
  • ROI Analyzer
    • ROIAnalyzer
  • ROI Classification Calculator - Single Core
    • ROIClfCalculator
  • ROI Classification Calculator - Multiprocess
    • ROIClfCalculatorMultiprocess
  • ROI Movement Analyzer - Single Core
    • ROIAggregateStatisticsAnalyzer
  • ROI Movement Analyzer - Multiprocess
    • ROIAggregateStatisticsAnalyzerMultiprocess
  • ROI Feature Analyzer
    • ROIFeatureCreator
  • ROI Directing Analyzer
    • DirectingROIAnalyzer
    • DirectingROIAnalyzer
  • ROI Time-Bin Calculator
    • ROITimebinAnalyzer
  • ROI Time-Bin Calculator (Legacy)
    • ROITimebinCalculator
  • ROI Size Standardizer
    • ROISizeStandardizer
• ROI Visualization
  • ROI Plotter - Single Core
    • ROIPlotter
  • ROI Plotter - Multiprocess
    • ROIPlotMultiprocess
  • ROI Feature Visualizer - Single Core
    • ROIfeatureVisualizer
  • ROI Feature Visualizer - Multiprocess
    • ROIfeatureVisualizerMultiprocess
  • ROI Directing Visualizer
    • DirectingROIVisualizer
• ROI GUI Tools
  • ROI GUI
    • ROI_ui
  • ROI GUI Mixin
    • ROI_mixin
  • ROI Ruler
    • ROIRuler
  • ROI GUI Utils
    • get_ear_tags_for_rectangle()
    • get_half_circle_vertices()
    • get_image_from_label()
    • get_roi_data()
    • get_roi_df_from_dict()
    • get_roi_dict_from_dfs()
    • get_triangle_vertices()
    • get_vertices_hexagon()
    • insert_gridlines_on_roi_img()
    • multiply_ROIs()
    • reset_video_ROIs()
    • set_roi_metric_sizes()
• ROI Shape Selectors
  • ROI Rectangle Selector
    • ROISelectorPolygon
  • ROI Circle Selector
    • ROISelectorCircle
  • ROI Polygon Selector
    • ROISelectorPolygon
  • ROI Rectangle Selector (Tkinter)
    • ROISelector
  • ROI Interactive Bufferer
    • InteractiveROIBufferer
• ROI Interactive Modifiers
  • ROI Interactive Modifier UI (Tkinter)
    • InteractiveROIModifier
  • ROI Interactive Modifier UI - Legacy (OpenCV)
    • InteractiveROIModifier
• ROI Data Import/Export
  • ROI CSV Importer
    • ROIDefinitionsCSVImporter

📊 Statistics transformations

Compute statistical features, drift, distances, and distribution comparisons in sliding or static time windows.

• Statistics mixin
  • Statistics
    • Statistics.adjusted_mutual_info()
    • Statistics.adjusted_rand()
    • Statistics.banfeld_raftery_index()
    • Statistics.bouguessa_wang_sun_v2()
    • Statistics.bray_curtis_dissimilarity()
    • Statistics.brunner_munzel()
    • Statistics.c_index()
    • Statistics.calinski_harabasz()
    • Statistics.chi_square()
    • Statistics.chow_test()
    • Statistics.circular_euclidean_kantorovich()
    • Statistics.cochrans_q()
    • Statistics.cohens_d()
    • Statistics.cohens_h()
    • Statistics.cohens_kappa()
    • Statistics.concordance_ratio()
    • Statistics.cop_index()
    • Statistics.cov_matrix()
    • Statistics.czebyshev_distance()
    • Statistics.d_prime()
    • Statistics.davis_bouldin()
    • Statistics.dunn_index()
    • Statistics.dunn_symmetry_idx()
    • Statistics.elliptic_envelope()
    • Statistics.eta_squared()
    • Statistics.find_collinear_features()
    • Statistics.fowlkes_mallows()
    • Statistics.geometric_mean()
    • Statistics.get_clustering_purity()
    • Statistics.gower_distance()
    • Statistics.grubbs_test()
    • Statistics.hamming_distance()
    • Statistics.hartley_fmax()
    • Statistics.hbos()
    • Statistics.hellinger_distance()
    • Statistics.i_index()
    • Statistics.independent_samples_t()
    • Statistics.isolation_forest()
    • Statistics.jaccard_distance()
    • Statistics.jensen_shannon_divergence()
    • Statistics.kendall_tau()
    • Statistics.kmeans_1d()
    • Statistics.kruskal_scipy()
    • Statistics.kruskal_wallis()
    • Statistics.krzanowski_lai_index()
    • Statistics.kullback_leibler_divergence()
    • Statistics.kumar_hassebrook_similarity()
    • Statistics.levenes()
    • Statistics.local_outlier_factor()
    • Statistics.mad_median_rule()
    • Statistics.mahalanobis_distance_cdist()
    • Statistics.manhattan_distance_cdist()
    • Statistics.mann_whitney()
    • Statistics.mclain_rao_index()
    • Statistics.mcnemar()
    • Statistics.normalized_google_distance()
    • Statistics.one_way_anova()
    • Statistics.one_way_anova_scipy()
    • Statistics.pairwise_tukeyhsd_scipy()
    • Statistics.pbm_index()
    • Statistics.pct_in_top_n()
    • Statistics.pearsons_r()
    • Statistics.phi_coefficient()
    • Statistics.population_stability_index()
    • Statistics.ray_turi_index()
    • Statistics.relative_risk()
    • Statistics.rmsstd()
    • Statistics.rolling_barletts_test()
    • Statistics.rolling_cohens_d()
    • Statistics.rolling_independent_sample_t()
    • Statistics.rolling_jensen_shannon_divergence()
    • Statistics.rolling_kullback_leibler_divergence()
    • Statistics.rolling_levenes()
    • Statistics.rolling_mann_whitney()
    • Statistics.rolling_one_way_anova()
    • Statistics.rolling_population_stability_index()
    • Statistics.rolling_shapiro_wilks()
    • Statistics.rolling_two_sample_ks()
    • Statistics.rolling_wasserstein_distance()
    • Statistics.s_dbw_index()
    • Statistics.scott_symons_index()
    • Statistics.sd_index()
    • Statistics.silhouette_score()
    • Statistics.sliding_autocorrelation()
    • Statistics.sliding_cumulative_mean()
    • Statistics.sliding_czebyshev_distance()
    • Statistics.sliding_dominant_frequencies()
    • Statistics.sliding_eta_squared()
    • Statistics.sliding_independent_samples_t()
    • Statistics.sliding_iqr()
    • Statistics.sliding_kendall_tau()
    • Statistics.sliding_kurtosis()
    • Statistics.sliding_mad_median_rule()
    • Statistics.sliding_pearsons_r()
    • Statistics.sliding_phi_coefficient()
    • Statistics.sliding_relative_risk()
    • Statistics.sliding_skew()
    • Statistics.sliding_spearman_rank_correlation()
    • Statistics.sliding_z_scores()
    • Statistics.sokal_michener()
    • Statistics.sokal_sneath()
    • Statistics.spearman_rank_correlation()
    • Statistics.symmetry_index()
    • Statistics.total_variation_distance()
    • Statistics.two_sample_ks()
    • Statistics.wasserstein_distance()
    • Statistics.wave_hedges_distance()
    • Statistics.wemmert_gancarski_index()
    • Statistics.wilcoxon()
    • Statistics.xie_beni()
    • Statistics.youden_j()
    • Statistics.yule_coef()
• Statistics GPU methods
  • adjusted_rand_gpu()
  • count_values_in_ranges()
  • davis_bouldin()
  • dunn_index()
  • euclidean_distance_to_static_point()
  • get_3pt_angle()
  • get_euclidean_distance_cuda()
  • get_euclidean_distance_cupy()
  • hamming_distance_gpu()
  • i_index()
  • kmeans_cuml()
  • kullback_leibler_divergence_gpu()
  • silhouette_score_gpu()
  • sliding_mean()
  • sliding_min()
  • sliding_spearmans_rank()
  • sliding_std()
  • sliding_sum()
  • sokal_sneath_gpu()
  • xie_beni()

📥 Third-party label appenders

Append labels from external annotation tools to pose-estimation outputs.

• BENTO
• BORIS
• BORIS source cleaner
• Deepethogram
• Ethovison
• Noldus Observer
• Solomon coder
• Shah appender
• Generic third-party appender tool
• Third-party annotation tools
• Annotation format converters
• COCO key-points -> YOLO pose-estimation format conversion
• COCO key-points -> YOLO bounding box conversion
• COCO key-points -> YOLO segmentation conversion
• SAM3 -> YOLO segmentation project
• SAM3 -> YOLO bounding-box (detection) project
• Merge multiple YOLO projects
• Multi-animal DeepLabCut predictions -> YOLO pose-estimation annotations format conversion
• DeepLabCut predictions -> YOLO pose-estimation annotations
• Lightning Pose annotations -> YOLO pose-estimation annotations
• Lightning Pose annotations -> YOLO bounding box annotations
• Merge Lightning Pose projects
• Crop Lightning Pose annotations
• Crop Lightning Pose annotations (bounding box square)
• Create Lightning Pose bounding box files
• Multi-animal DeepLabCut -> YOLO pose-estimation annotations
• DeepLabCut single-to-multi-animal format converter
• DeepLabCut annotations -> Labelme annotations
• Labelme annotations -> DeepLabCut annotations
• Labelme annotations -> DataFrame
• Labelme annotations -> DeepLabCut annotations
• Labelme annotations -> YOLO bounding box annotations
• Labelme points -> YOLO keypoints annotations
• Labelme points -> YOLO segmentation annotations
• SimBA ROIs -> YOLO bounding box annotations
• SimBA pose-estimation -> YOLO pose-estimation annotations
• SLEAP CSV predictions -> YOLO pose-estimation annotations
• SLEAP H5 predictions -> YOLO pose-estimation annotations
• SLEAP annotations -> YOLO pose-estimation annotations
• Annotation conversion utilities

🕐 Time-series transformations

Analyze time-series complexity using sliding window methods.

• Time-series statistics mixin
  • TimeseriesFeatureMixin
    • TimeseriesFeatureMixin.acceleration()
    • TimeseriesFeatureMixin.avg_kinetic_energy()
    • TimeseriesFeatureMixin.benford_correlation()
    • TimeseriesFeatureMixin.crossings()
    • TimeseriesFeatureMixin.dominant_frequencies()
    • TimeseriesFeatureMixin.entropy_of_directional_changes()
    • TimeseriesFeatureMixin.granger_tests()
    • TimeseriesFeatureMixin.higuchi_fractal_dimension()
    • TimeseriesFeatureMixin.hjort_parameters()
    • TimeseriesFeatureMixin.line_length()
    • TimeseriesFeatureMixin.linearity_index()
    • TimeseriesFeatureMixin.local_maxima_minima()
    • TimeseriesFeatureMixin.longest_strike()
    • TimeseriesFeatureMixin.mean_squared_jerk()
    • TimeseriesFeatureMixin.momentum_magnitude()
    • TimeseriesFeatureMixin.path_aspect_ratio()
    • TimeseriesFeatureMixin.path_curvature()
    • TimeseriesFeatureMixin.percent_beyond_n_std()
    • TimeseriesFeatureMixin.percent_in_percentile_window()
    • TimeseriesFeatureMixin.percentile_difference()
    • TimeseriesFeatureMixin.permutation_entropy()
    • TimeseriesFeatureMixin.petrosian_fractal_dimension()
    • TimeseriesFeatureMixin.radial_dispersion_index()
    • TimeseriesFeatureMixin.radial_eccentricity()
    • TimeseriesFeatureMixin.sliding_avg_kinetic_energy()
    • TimeseriesFeatureMixin.sliding_benford_correlation()
    • TimeseriesFeatureMixin.sliding_crossings()
    • TimeseriesFeatureMixin.sliding_descriptive_statistics()
    • TimeseriesFeatureMixin.sliding_displacement()
    • TimeseriesFeatureMixin.sliding_entropy_of_directional_changes()
    • TimeseriesFeatureMixin.sliding_hjort_parameters()
    • TimeseriesFeatureMixin.sliding_line_length()
    • TimeseriesFeatureMixin.sliding_linearity_index()
    • TimeseriesFeatureMixin.sliding_longest_strike()
    • TimeseriesFeatureMixin.sliding_mean_squared_jerk()
    • TimeseriesFeatureMixin.sliding_momentum_magnitude()
    • TimeseriesFeatureMixin.sliding_path_aspect_ratio()
    • TimeseriesFeatureMixin.sliding_path_curvature()
    • TimeseriesFeatureMixin.sliding_pct_in_top_n()
    • TimeseriesFeatureMixin.sliding_percent_beyond_n_std()
    • TimeseriesFeatureMixin.sliding_percent_in_percentile_window()
    • TimeseriesFeatureMixin.sliding_percentile_difference()
    • TimeseriesFeatureMixin.sliding_petrosian_fractal_dimension()
    • TimeseriesFeatureMixin.sliding_spatial_density()
    • TimeseriesFeatureMixin.sliding_stationary()
    • TimeseriesFeatureMixin.sliding_two_signal_crosscorrelation()
    • TimeseriesFeatureMixin.sliding_unique()
    • TimeseriesFeatureMixin.sliding_variance()
    • TimeseriesFeatureMixin.sliding_window_stats()
    • TimeseriesFeatureMixin.spatial_density()
    • TimeseriesFeatureMixin.spike_finder()
    • TimeseriesFeatureMixin.spike_train_finder()
    • TimeseriesFeatureMixin.time_since_previous_target_value()
    • TimeseriesFeatureMixin.time_since_previous_threshold()
• Time-series statistics GPU methods
  • sliding_hjort_parameters_gpu()
  • sliding_linearity_index_cuda()
  • sliding_percent_beyond_n_std()
  • sliding_spatial_density_cuda()
  • sliding_threshold()

🔮 Unsupervised learning

Clustering and dimensionality reduction methods for behavioral analysis.

• Bout aggregation helper
  • bout_aggregator()
• Cluster frequentist statistics calculator
  • ClusterFrequentistCalculator
• Cluster video visualizer
  • ClusterVideoVisualizer
• Cluster XAI calculator
  • ClusterXAICalculator
• Data extractor
  • DataExtractor
• Data creator
  • DatasetCreator
• Density-based cluster validation (DBCV)
  • DBCVCalculator
• Embedding correlation calculator
  • EmbeddingCorrelationCalculator
• Grid-search visualizer
  • GridSearchVisualizer
• HDBSCAN clusterer
  • HDBSCANClusterer
• UMAP embedder
  • UmapEmbedder
• Unsupervised mixins

🖥️ User Interface (UI) tools

SimBA’s GUI components and window-based interaction logic.

• Create project UI
• Set machine learning hyperparameters UI
• SimBA ML settings frame
• SimBA tkinter methods
• SimBA create user-defined pose config UI
• SimBA set video info UI
• SimBA video timelapse
• SimBA import pose frame
• SimBA import videos frame
• SimBA batch process menus
• SimBA get pixels per millimeter converstion UI
• SimBA pop-up UIs
• SimBA pop-up mixin

⚙️ Utilities

Helper methods for logging, CLI execution, argument checks, warnings, and I/O.

• SimBA argument checks
• SimBA project config creator
• Data utilities
• SimBA Enumerals
• SimBA Errors
• Lookups
• SimBA Printing
• Reading and writing
• SimBA Warnings
• SimBA CLI tools

📹 Video processing tools

Video processing tools using OpenCV and FFmpeg.

• Video processing tools
  • VideoRotator
    • VideoRotator.run()
  • append_audio()
  • batch_convert_video_format()
  • batch_create_frames()
  • batch_video_to_greyscale()
  • change_fps_of_multiple_videos()
  • change_img_format()
  • change_playback_speed()
  • change_playback_speed_dir()
  • change_single_video_fps()
  • clahe_enhance_video()
  • clahe_enhance_video_mp()
  • clip_video_in_range()
  • clip_videos_by_frame_ids()
  • convert_to_avi()
  • convert_to_bmp()
  • convert_to_jpeg()
  • convert_to_mov()
  • convert_to_mp4()
  • convert_to_png()
  • convert_to_tiff()
  • convert_to_webm()
  • convert_to_webp()
  • convert_video_powerpoint_compatible_format()
  • copy_img_folder()
  • create_average_frm()
  • create_blank_video()
  • crop_multiple_videos()
  • crop_multiple_videos_circles()
  • crop_multiple_videos_polygons()
  • crop_single_video()
  • crop_single_video_circle()
  • crop_single_video_polygon()
  • crop_video()
  • crossfade_two_videos()
  • downsample_video()
  • extract_frame_range()
  • extract_frames_from_all_videos_in_directory()
  • extract_frames_single_video()
  • flip_videos()
  • frames_to_movie()
  • get_async_frame_batch()
  • get_img_slic()
  • get_video_slic()
  • gif_creator()
  • horizontal_video_concatenator()
  • is_video_seekable()
  • mixed_mosaic_concatenator()
  • mosaic_concatenator()
  • multi_split_video()
  • reencode_mp4_video()
  • remove_beginning_of_video()
  • remove_end_of_video()
  • resize_videos_by_height()
  • resize_videos_by_width()
  • reverse_videos()
  • roi_blurbox()
  • rotate_video()
  • split_mosaic()
  • superimpose_elapsed_time()
  • superimpose_frame_count()
  • superimpose_freetext()
  • superimpose_overlay_video()
  • superimpose_video_names()
  • superimpose_video_progressbar()
  • temporal_concatenation()
  • upsample_fps()
  • vertical_video_concatenator()
  • video_bg_subtraction()
  • video_bg_subtraction_mp()
  • video_concatenator()
  • video_to_bw()
  • video_to_greyscale()
  • watermark_video()
• Multi-cropper
• Crop ROI selector (rectangles)
• Crop ROI selector (circles)
• Crop ROI selector (polygons)
• Interactive CLAHE
  • interactive_clahe_ui()
• Interactive brightness / contrast
  • BrightnessContrastUI
• Batch video process executor
  • FFMPEGCommandCreator
• Egocentrically rotate videos
  • EgocentricVideoRotator
• Asynchronous frame reader
  • AsyncVideoFrameReader
  • get_async_frame_batch()
• Asynchronous frame reader (GPU)

👁️ YOLO Methods

Methods for training YOLO models, creating training and validation datasets, and converting behavioral neuroscience-specific datasets to YOLO datasets.

Uses the Ultralytics package.

• YOLO methods
  • Utilities
  • Bounding-box inference
  • NVDEC GPU-accelerated YOLO inference
  • Pose-estimation inference
  • YOLO pose-estimation segmentation visualizer
  • YOLO pose-estimation segmentation inference
  • Pose-estimation track inference
  • Pose-estimation track plotting
  • Pose-estimation plotting
  • Bounding box plotting
  • YOLO annotation visualizer
  • COCO key-points -> YOLO pose-estimation format conversion
  • COCO key-points -> YOLO bounding box conversion
  • COCO key-points -> YOLO segmentation conversion
  • SAM3 -> YOLO segmentation project
  • SAM3 -> YOLO bounding-box (detection) project
  • Merge multiple YOLO projects
  • Multi-animal DeepLabCut predictions -> YOLO pose-estimation annotations format conversion
  • DeepLabCut predictions -> YOLO pose-estimation annotations
  • Labelme annotations -> YOLO bounding box annotations
  • Labelme points -> YOLO keypoints annotations
  • Labelme points -> YOLO segmentation annotations
  • SimBA ROIs -> YOLO bounding box annotations
  • SimBA pose-estimation -> YOLO pose-estimation annotations
  • SimBA pose-estimation -> YOLO segmentation annotations
  • SLEAP CSV predictions -> YOLO pose-estimation annotations
  • SLEAP H5 predictions -> YOLO pose-estimation annotations
  • SLEAP annotations -> YOLO pose-estimation annotations
  • LightningPose keypoints -> YOLO bounding box conversion
  • LightningPose keypoints -> YOLO pose-estimation annotations