YORU: animal behavior detection with object-based approach for real-time closed-loop feedback

Fig.2B

• Drawing a graph: draw_ethogram_wing_extension.R

Fig.2C

• Plotting: wing_extension_APs_analysis.R

Fig.2E

• Drawing a graph: draw_ethogram_trophallaxis.R

Fig.2F

• Plotting: trophallaxis_APs_analysis.R

Fig.2H

• Drawing a graph: draw_ethogram_orientation.R

Fig.2I

• Plotting: orientation_APs_analysis.R

Fig.2K

• Plotting: group_wing_extension_APs_analysis.R

Fig.2M

• Plotting: group_trophallaxis_APs_analysis.R

Fig.4C

• Plotting: real_time_latency_model_analysis.R

Fig.4D

• Plotting: real_time_latency_fps_analysis.R

Fig.5D

• Plotting: wing_extension_amount_pIP10.R

Fig.5E

• Plotting: cumulative_copulation_rate_pIP10.R

Fig.6F

• Plotting: cumulative_copulation_rate_JO15-2.R

Fig.S2A to C

• Plotting: other_dataset_bar_graph.ipynb

Fig.S2D

• Plotting: behavior_freq_analysis_plots.py

Fig.S3C

• Plotting: expoert_evaluation_graph_flies.py

Fig.S3D

• Plotting: expoert_evaluation_graph_ants.py

Fig.S4A

• Plotting: plot_compare_keypoint_moseq_wing_extension.py

Fig.S4B and D

• Plotting: plot_f1_bar_graph_all.py

Related to Table S3 and S4

Fig.S4C

• Plotting: plot_compare_keypoint_moseq_trophallaxis.py

Fig.S5A

• Plotting: plot_total_bar_with_groups_bw_ant.py

Related to Table S5

Fig.S5B

• Plotting: plot_total_bar_with_groups_bw_ants.py

Related to Table S6

Fig.S6A to C, 8A and B

• Plotting: draw_precision_recall_bar_graph.R

Related to Table S7

Fig.S7A

• Plotting: wing_extension_IOUs_analysis.R

Fig.S7B

• Plotting: trophallaxis_IOUs_analysis.R

Fig.S7C

• Plotting: orientation_IOUs_analysis.R

Fig.S8C

• Plotting: group_wing_extension_IOUs_analysis.R

Fig.S8D

• Plotting: group_trophallaxis_IOUs_analysis.R

Fig.S9B

• Plotting: individual_no_plotting_line.R

Fig.S10A

• Plotting: plot_bar_graph_with_other_object_detection_algorithm.ipynb

Fig.S10B

• Plotting: wing_fly_AP_graph_object_detection.R

Fig.S10C

• Plotting: ant_tro_AP_graph_other_object_detection.R

Fig.S10D

• Plotting: zebra_orientation_AP_graph_object_detection.R

Fig.S10E

• Plotting: group_wing_fly_AP_graph_object_detection.R

Fig.S10F

• Plotting: group_tro_ant_AP_graph_object_detection.R

Fig.S11

• Plotting: mouse_behavior_IOUs_analysis.R

Fig.S13B

• Plotting: inference_speed_analysis.R

Fig.S14A

• Plotting: real_time_latency_memory_analysis.R

Fig.S14B

• Plotting: real_time_latency_camera_analysis.R

Fig.S14C

• Plotting: real_time_latency_trigger_analysis.R

Fig.S15C

• Plotting: model_onset_latency_analysis_with_SLEAP.R

Table S1

• Calculate accuracy score (Mouse-Ventral1): mouse_ventral1_yoru_analysis.ipynb
• Calculate accuracy score (Mouse-Ventral2): mouse_ventral2_yoru_analysis.ipynb
• Calculate accuracy score (CalM21): CalM21_dataset_yoru_analysis.py

Table S2

• Calculate accuracy score (Fly - wing extension): wing_extension_BORIS_data_reshape_analysis.ipynb
• Calculate accuracy score (Ant - trophallaxis): trophallaxis_BORIS_data_reshape_analysis.ipynb
• Calculate accuracy score (Zebrafish - orientation): orientation_BORIS_data_reshape_analysis.ipynb

Table S3

• Calculate accuracy score: wing_extension_keypointmoseq_data_reshape_analysis.ipynb

Table S4

• Calculate accuracy score: trophallaxis_keypointmoseq_data_reshape_analysis.ipynb

Table S5

• Calculate accuracy score (A-SOiD): wing_extension_asoid_data_reshape_analysis.ipynb
• Calculate accuracy score (YORU): cross_validation_wing_extension_YORU.py

Table S6

• Calculate accuracy score (A-SOiD): trophallaxis_asoid_data_reshape_analysis.ipynb
• Calculate accuracy score (YORU): cross_validation_trophallaxis_YORU.py

Table S11

• Calculate inference speed: YOLO_latency_compared_to_GPUs.ipynb

SLEAP real-time analysis program

• System: sleap_real_time_task_program.py
• Arduino Firmata program: arduino.py