Contents:

  • Installation
    • Recommended System Requirements
    • Installation
    • Compile it yourself
      • Local conda channel
      • Compiling manually (TODO)
      • Special needs
      • Basler Pylon support
  • Workflow & Quick Start
    • Command-Line
    • On Video Files and File Sizes
  • Tutorials
    • Understanding Computational Complexity
      • Parameters
    • Tutorial: Basics
      • Setting Up a New Project
      • The Graphical Interface
      • Parameter Optimizations
      • Tracklets
    • Correcting Tracking Mistakes
      • Correcting Manually
      • Automatic Visual Identification
    • Posture
    • Tutorial: Machine-learning based pose detection
      • Setting Up a New Project
      • Improving Visuals
      • Adjusting Posture Based On Keypoints
      • Finally
  • Training your own model
    • Introduction
    • Setting Up the Environment
    • Data Preparation
    • Configuring YOLOv11
    • Troubleshooting and Tips
  • Basic Command-line Usage
    • Basic principles & Good practices
    • Using settings files
    • Setting parameters in the correct order
    • Other command-line tools
    • Run software directly using shortcuts
  • Updating the App
    • Installed using conda
    • conda-integrated update mechanism
    • Installed manually
  • Usage examples
    • Command-line
      • TRex: general usage examples
      • Create tracklet images to use with other posture estimation software
      • Create a short clip of objects with or w/o background after converting to PV
    • Closed-loop
  • Using the graphical user interface
    • Keyboard shortcuts
    • Timeline
    • Changing the cm/px conversion factor
    • Display menu
    • Excluding regions / tracking specific regions exclusively
    • Manually assigning individuals
  • Batch processing support
  • Examples
  • File formats
    • Positional Data
    • Posture-data
    • Tracklet images
      • Open all images of a certain individual ID
      • Now we want to see that for all individuals
      • We can now map from segments (meta) to tracklet images from the big file
      • Further examples
    • Visual fields
    • Heatmaps
    • PreprocessedVideo (pv)
  • TRex parameters
    • accumulation_enable()
    • accumulation_enable_final_step()
    • accumulation_max_tracklets()
    • accumulation_sufficient_uniqueness()
    • accumulation_tracklet_add_factor()
    • adaptive_threshold_scale()
    • analysis_range()
    • app_check_for_updates()
    • app_last_update_version()
    • approximate_length_minutes()
    • auto_apply()
    • auto_categorize()
    • auto_minmax_size()
    • auto_no_memory_stats()
    • auto_no_outputs()
    • auto_no_results()
    • auto_no_tracking_data()
    • auto_number_individuals()
    • auto_quit()
    • auto_tags()
    • auto_train()
    • auto_train_dont_apply()
    • average_samples()
    • averaging_method()
    • blob_size_range()
    • blob_split_algorithm()
    • blob_split_global_shrink_limit()
    • blob_split_max_shrink()
    • blobs_per_thread()
    • blur_difference()
    • calculate_posture()
    • cam_circle_mask()
    • cam_framerate()
    • cam_limit_exposure()
    • cam_matrix()
    • cam_resolution()
    • cam_scale()
    • cam_undistort()
    • cam_undistort_vector()
    • categories_apply_min_tracklet_length()
    • categories_ordered()
    • categories_train_min_tracklet_length()
    • closed_loop_enable()
    • closed_loop_path()
    • closing_size()
    • cm_per_pixel()
    • color_channel()
    • correct_illegal_lines()
    • correct_luminance()
    • crop_offsets()
    • crop_window()
    • data_prefix()
    • debug_recognition_output_all_methods()
    • detect_batch_size()
    • detect_classes()
    • detect_conf_threshold()
    • detect_format()
    • detect_iou_threshold()
    • detect_keypoint_names()
    • detect_model()
    • detect_only_classes()
    • detect_precomputed_file()
    • detect_size_filter()
    • detect_skeleton()
    • detect_threshold()
    • detect_threshold_is_absolute()
    • detect_tile_image()
    • detect_type()
    • dilation_size()
    • enable_difference()
    • equalize_histogram()
    • evaluate_thresholds()
    • event_min_peak_offset()
    • exec()
    • ffmpeg_crf()
    • ffmpeg_path()
    • filename()
    • frame_rate()
    • gpu_learning_rate()
    • gpu_max_cache()
    • gpu_max_epochs()
    • gpu_max_sample_gb()
    • gpu_min_elements()
    • gpu_min_iterations()
    • gpu_torch_device()
    • gpu_torch_device_index()
    • gpu_torch_no_fixes()
    • gpu_verbosity()
    • grabber_force_settings()
    • grid_points()
    • grid_points_scaling()
    • gui_auto_scale()
    • gui_auto_scale_focus_one()
    • gui_background_color()
    • gui_blob_label()
    • gui_connectivity_matrix()
    • gui_connectivity_matrix_file()
    • gui_displayed_frame()
    • gui_draw_blobs_separately()
    • gui_draw_only_filtered_out()
    • gui_equalize_blob_histograms()
    • gui_faded_brightness()
    • gui_fish_color()
    • gui_fish_label()
    • gui_focus_group()
    • gui_foi_name()
    • gui_frame()
    • gui_happy_mode()
    • gui_highlight_categories()
    • gui_macos_blur()
    • gui_max_path_time()
    • gui_mode()
    • gui_outline_thickness()
    • gui_playback_speed()
    • gui_pose_smoothing()
    • gui_recording_format()
    • gui_run()
    • gui_show_autoident_controls()
    • gui_show_blobs()
    • gui_show_boundary_crossings()
    • gui_show_cliques()
    • gui_show_dataset()
    • gui_show_detailed_probabilities()
    • gui_show_export_options()
    • gui_show_fish()
    • gui_show_graph()
    • gui_show_heatmap()
    • gui_show_histograms()
    • gui_show_inactive_individuals()
    • gui_show_individual_preview()
    • gui_show_infocard()
    • gui_show_match_modes()
    • gui_show_matching_info()
    • gui_show_memory_stats()
    • gui_show_midline()
    • gui_show_midline_histogram()
    • gui_show_misc_metrics()
    • gui_show_number_individuals()
    • gui_show_only_unassigned()
    • gui_show_outline()
    • gui_show_paths()
    • gui_show_pixel_grid()
    • gui_show_posture()
    • gui_show_probabilities()
    • gui_show_processing_time()
    • gui_show_recognition_bounds()
    • gui_show_recognition_summary()
    • gui_show_selections()
    • gui_show_shadows()
    • gui_show_skeletons()
    • gui_show_texts()
    • gui_show_timeline()
    • gui_show_timing_stats()
    • gui_show_uniqueness()
    • gui_show_video_background()
    • gui_show_visualfield()
    • gui_show_visualfield_ts()
    • gui_single_identity_color()
    • gui_timeline_alpha()
    • gui_wait_for_background()
    • gui_wait_for_pv()
    • gui_zoom_limit()
    • gui_zoom_polygon()
    • heatmap_dynamic()
    • heatmap_frames()
    • heatmap_ids()
    • heatmap_normalization()
    • heatmap_resolution()
    • heatmap_smooth()
    • heatmap_source()
    • heatmap_value_range()
    • history_matching_log()
    • huge_timestamp_seconds()
    • image_adjust()
    • image_brightness_increase()
    • image_contrast_increase()
    • image_invert()
    • image_square_brightness()
    • individual_image_normalization()
    • individual_image_scale()
    • individual_image_size()
    • individual_names()
    • individual_prefix()
    • individuals_per_thread()
    • limit()
    • log_file()
    • manual_matches()
    • manual_splits()
    • manually_approved()
    • mask_path()
    • match_min_probability()
    • match_mode()
    • meta_age_days()
    • meta_conditions()
    • meta_conversion_time()
    • meta_encoding()
    • meta_mass_mg()
    • meta_misc()
    • meta_real_width()
    • meta_source_path()
    • meta_species()
    • meta_video_scale()
    • meta_video_size()
    • meta_write_these()
    • midline_invert()
    • midline_resolution()
    • midline_start_with_head()
    • midline_stiff_percentage()
    • midline_walk_offset()
    • nowindow()
    • outline_approximate()
    • outline_compression()
    • outline_curvature_range_ratio()
    • outline_resample()
    • outline_smooth_samples()
    • outline_smooth_step()
    • outline_use_dft()
    • output_annotations()
    • output_auto_detection_fields()
    • output_auto_pose()
    • output_centered()
    • output_csv_decimals()
    • output_default_options()
    • output_dir()
    • output_fields()
    • output_format()
    • output_frame_window()
    • output_heatmaps()
    • output_interpolate_positions()
    • output_invalid_value()
    • output_min_frames()
    • output_normalize_midline_data()
    • output_origin()
    • output_posture_data()
    • output_prefix()
    • output_recognition_data()
    • output_statistics()
    • output_tracklet_images()
    • output_visual_fields()
    • panic_button()
    • peak_mode()
    • pose_midline_indexes()
    • posture_closing_size()
    • posture_closing_steps()
    • posture_direction_smoothing()
    • posture_head_percentage()
    • postures_per_thread()
    • python_path()
    • quit_after_average()
    • recognition_border()
    • recognition_border_shrink_percent()
    • recognition_border_size_rescale()
    • recognition_coeff()
    • recognition_save_progress_images()
    • recognition_shapes()
    • recognition_smooth_amount()
    • recording()
    • region_model()
    • reset_average()
    • save_raw_movie()
    • save_raw_movie_path()
    • settings_file()
    • smooth_window()
    • solid_background_color()
    • source()
    • speed_extrapolation()
    • stop_after_minutes()
    • system_memory_limit()
    • tags_approximation()
    • tags_debug()
    • tags_dont_track()
    • tags_enable()
    • tags_equalize_hist()
    • tags_image_size()
    • tags_maximum_image_size()
    • tags_model_path()
    • tags_num_sides()
    • tags_path()
    • tags_recognize()
    • tags_save_predictions()
    • tags_saved_only()
    • tags_size_range()
    • tags_threshold()
    • task()
    • terminate_training()
    • test_image()
    • threshold_maximum()
    • threshold_ratio_range()
    • track_background_subtraction()
    • track_conf_threshold()
    • track_consistent_categories()
    • track_do_history_split()
    • track_enforce_frame_rate()
    • track_history_split_threshold()
    • track_ignore()
    • track_ignore_bdx()
    • track_include()
    • track_intensity_range()
    • track_max_individuals()
    • track_max_reassign_time()
    • track_max_speed()
    • track_only_categories()
    • track_only_classes()
    • track_only_segmentations()
    • track_pause()
    • track_posture_threshold()
    • track_size_filter()
    • track_speed_decay()
    • track_threshold()
    • track_threshold_2()
    • track_threshold_is_absolute()
    • track_time_probability_enabled()
    • track_trusted_probability()
    • tracklet_force_normal_color()
    • tracklet_max_images()
    • tracklet_max_length()
    • tracklet_normalize()
    • tracklet_punish_speeding()
    • tracklet_punish_timedelta()
    • use_adaptive_threshold()
    • use_closing()
    • use_differences()
    • video_conversion_range()
    • video_length()
    • video_reading_use_threads()
    • video_size()
    • video_source()
    • visual_field_eye_offset()
    • visual_field_eye_separation()
    • visual_field_history_smoothing()
    • visual_field_shapes()
    • visual_identification_model_path()
    • visual_identification_save_images()
    • visual_identification_version()
    • web_quality()
    • web_time_threshold()
    • webcam_index()
    • yolo_region_tracking_enabled()
    • yolo_tracking_enabled()
  • Frequently Asked Questions
    • I am using Windows and Python cannot be initialized successfully!
    • Trajectories jump around a lot for no particular reason!
    • Tracking is really slow!
    • 🦖 does not quit and seems to be stuck!
    • I am getting a GLIBCXX_3.X.XX (e.g. GLIBCXX_3.4.30) error on Linux.
TRex
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