MPD: Data set: Kumar4

Sheppard K, Gardin J, Sabnis GS, Peer A, Darrell M, Deats S, Geuther B, Lutz CM, Kumar V. Stride-level analysis of mouse open field behavior using deep-learning-based pose estimation. Cell Rep. 2022 Jan 11;38(2):110231. doi: 10.1016/j.celrep.2021.110231. PubMed 35021077

A novel method for the measurement of posture and its effect on gait, an important indicator of neural function, was studied in 52 inbred mice strains and 10 F1 hybrid lines. The basics of this toolkit is a deep convolutional neural network trained to perform pose estimation on top-down video of an open field test. This network provided twelve 2D-dimensional markers of various mouse anatomical locations, or key points, for each frame of video that described the pose of the mouse at each time point; that allowed the processing of this time series of poses and identifying poses that represent individual strides. This facilitated the extraction of several significant gait metrics, and mean, median and variance are provided for each metric.

Experimental groups in this study:
• Baseline

Procedures conducted:

• body size and weight		Body length measurements.
• open field test		Distance traveled.
• gait analysis		Angular velocity, Stride speed, Step length, Step width, and other gait metrics.

Kumar4 downloads
• Download Kumar4 project data set animal data, as uploaded
• Download Kumar4 animal data matrix with factor-related expansion applied as necessary
• Download Kumar4 strain means, SD, N, etc. one row per strain/sex/measure

Ontology terms mapped to Kumar4 measures:

MA:0000008 tail
MA:0000026 hindlimb
MA:0000044 foot
MA:0000281 nose
MA:0002848 tail tip
MP:0001256 abnormal body length
MP:0001392 abnormal locomotor behavior
MP:0001406 abnormal gait
VT:0001256 body length
VT:0010730 locomotor coordination trait
VT:0010731 gait trait

Investigators	Vivek Kumar The Jackson Laboratory, Bar Harbor, ME
Participants	Sheppard K, Gardin J, Sabnis GS, Peer A, Darrell M, Deats S, Geuther B, Lutz CM
Contact	Vivek Kumar vivek.kumar@jax.org Lab web site
Funding Provided By	NIH DA041668, DA048634; The Jackson Laboratory Directors Innovation Fund; Brain and Behavioral Foundation Young Investigator Award
Project type	Phenotype strain survey data set
MPD identifiers	Kumar4 MPD:1102
Data changelog	No updates/corrections. Initial release date: 12/2021.
Formatted citation	Click above to copy-paste the entire citation for this MPD web page.

Sort/ Pick	Data set	Procedure / Protocol	Treatment	Phenotype Measure / Variable (click to view)	Panel	No. of Strains	Sex	Age	Sample Size (Avg)
Kumar4:2	Kumar4	body size and weight	(none)	distance from base of neck keypoint to center spine keypoint, plus center spine keypoint to base of tail keypoint, median [cm] body_length 114432	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:3	Kumar4	open field test	(none)	distance traveled during approximately one hour test [cm] distance 114433	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:4	Kumar4	gait analysis	(none)	number of strides, hind paws (keypoints) [n] stride_count 114434	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:5	Kumar4	gait analysis	(none)	angular velocity over duration of stride, mean [deg/s] angular_velocity_mean 114435	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:6	Kumar4	gait analysis	(none)	angular velocity over duration of stride, median [deg/s] angular_velocity_median 114436	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:7	Kumar4	gait analysis	(none)	angular velocity over duration of stride, variance [deg/s] angular_velocity_var 114437	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:8	Kumar4	gait analysis	(none)	lateral displacement of base of tail keypoint, mean base_tail_lateral_displacement_mean 114438	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:9	Kumar4	gait analysis	(none)	lateral displacement of base of tail keypoint, median base_tail_lateral_displacement_median 114439	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:10	Kumar4	gait analysis	(none)	lateral displacement of base of tail keypoint, variance base_tail_lateral_displacement_var 114440	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:11	Kumar4	gait analysis	(none)	limb duty factor, hind paws (keypoints), mean limb_duty_factor_mean 114441	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:12	Kumar4	gait analysis	(none)	limb duty factor, hind paws (keypoints), median limb_duty_factor_median 114442	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:13	Kumar4	gait analysis	(none)	limb duty factor, hind paws (keypoints), variance limb_duty_factor_var 114443	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:14	Kumar4	gait analysis	(none)	lateral displacement of nose keypoint, mean nose_lateral_displacement_mean 114444	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:15	Kumar4	gait analysis	(none)	lateral displacement of nose keypoint, median nose_lateral_displacement_median 114445	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:16	Kumar4	gait analysis	(none)	lateral displacement of nose keypoint, variance nose_lateral_displacement_var 114446	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:17	Kumar4	gait analysis	(none)	base tail keypoint speed, mean [cm/s] speed_mean 114447	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:18	Kumar4	gait analysis	(none)	base tail keypoint speed, median [cm/s] speed_median 114448	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:19	Kumar4	gait analysis	(none)	base tail keypoint speed, variance [cm/s] speed_var 114449	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:20	Kumar4	gait analysis	(none)	distance right hind paw keypoint travels past previous left hind paw keypoint strike, mean [cm] step_length1_mean 114450	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:21	Kumar4	gait analysis	(none)	distance right hind paw keypoint travels past previous left hind paw keypoint strike, median [cm] step_length1_median 114451	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:22	Kumar4	gait analysis	(none)	distance right hind paw keypoint travels past previous left hind paw keypoint strike, variance [cm] step_length1_var 114452	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:23	Kumar4	gait analysis	(none)	distance left hind paw keypoint travels past the right hind paw keypoint strike, mean [cm] step_length2_mean 114453	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:24	Kumar4	gait analysis	(none)	distance left hind paw keypoint travels past the right hind paw keypoint strike, median [cm] step_length2_median 114454	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:25	Kumar4	gait analysis	(none)	distance left hind paw keypoint travels past the right hind paw keypoint strike, variance [cm] step_length2_var 114455	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:26	Kumar4	gait analysis	(none)	lateral distance separating hind paws (keypoints), mean [cm] step_width_mean 114456	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:27	Kumar4	gait analysis	(none)	lateral distance separating hind paws (keypoints), median [cm] step_width_median 114457	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:28	Kumar4	gait analysis	(none)	lateral distance separating hind paws (keypoints), variance [cm] step_width_variance 114458	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:29	Kumar4	gait analysis	(none)	distance left hind paw keypoint travels for a stride, from toe-off to foot-strike, mean [cm] stride_length_mean 114459	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:30	Kumar4	gait analysis	(none)	distance left hind paw keypoint travels for a stride, from toe-off to foot-strike, median [cm] stride_length_median 114460	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:31	Kumar4	gait analysis	(none)	distance left hind paw keypoint travels for a stride, from toe-off to foot-strike, variance [cm] stride_length_var 114461	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:32	Kumar4	gait analysis	(none)	temporal symmetry of limb duty factor of hind paws (keypoints), mean temporal_symmetry_mean 114462	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:33	Kumar4	gait analysis	(none)	temporal symmetry of limb duty factor of hind paws (keypoints), median temporal_symmetry_median 114463	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:34	Kumar4	gait analysis	(none)	temporal symmetry of limb duty factor of hind paws (keypoints), variance temporal_symmetry_var 114464	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:35	Kumar4	gait analysis	(none)	lateral displacement of tip of tail keypoint, mean tip_tail_lateral_displacement_mean 114465	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:36	Kumar4	gait analysis	(none)	lateral displacement of tip of tail keypoint, median tip_tail_lateral_displacement_median 114466	inbred w/CC8	62	both	10-20wks	N=19

Kumar4:37	Kumar4	gait analysis	(none)	lateral displacement of tip of tail keypoint, variance tip_tail_lateral_displacement_variance 114467	inbred w/CC8	62	both	10-20wks	N=19

Kumar4: Gait and whole body posture measures in 52 inbred strains of mice and 10 F1 hybrid lines (2021)