Related Software

A non-exhaustive map of the animal pose-estimation, tracking, and behavior-analysis ecosystem that SimBA is commonly used alongside, grouped by primary purpose. Many tools span several categories; each is listed under its main use.

Pose estimation

Software	Type	Description
DeepLabCut	Open source	Markerless 2D/3D pose estimation
SLEAP	Open source	Multi-animal pose estimation
DeepPoseKit	Open source	Pose estimation toolkit
Lightning Pose	Open source	Semi-supervised, multi-view pose estimation
Facemap	Open source	Mouse orofacial tracking and neural prediction
OpenPose	Open source	Real-time multi-person 2D keypoint detection
MMPose	Open source	General-purpose pose estimation toolbox (OpenMMLab)
YOLO (Ultralytics)	Open source	Real-time keypoint/pose estimation (SimBA-supported); also object detection and segmentation

3D pose estimation

Software	Type	Description
DeepFly3D	Open source	3D pose estimation for tethered Drosophila
Anipose	Open source	3D pose estimation from synchronized cameras
DANNCE	Open source	3D landmark detection from multi-view video

Tracking and identity

Software	Type	Description
TRex	Open source	Real-time, identity-preserving tracking
idtracker.ai	Open source	Markerless identity tracking for animal groups
AlphaTracker	Open source	Multi-animal tracking, pose, and behavioral clustering
Tracktor	Open source	OpenCV-based single- and multi-object tracker
ToxTrac	Open source	Fast tracker for one or several animals
ezTrack	Open source	Blob-based location and freezing tracking
LiveMouseTracker	Open source	Long-term mouse tracking via RFID and depth cameras
TrackMate	Open source	ImageJ/Fiji object-tracking plugin
C-Trax	Open source	Tracking of walking flies in groups

Supervised behavior classification

Software	Type	Description
JAABA	Open source	Supervised behavior classification from trajectories
DeepEthogram	Open source	Supervised behavior classification from raw video
MARS	Open source	Pose estimation and social behavior classification in mice
BehaviorDEPOT	Open source	Pose-guided behavior detection and analysis
LabGym	Open source	Tracking and behavior classification via Mask R-CNN
SIPEC	Open source	End-to-end deep-learning behavioral analysis pipeline

Unsupervised behavior discovery

Software	Type	Description
B-SOID	Open source	Unsupervised behavior discovery from pose
A-SOID	Open source	Active-learning behavior classification from pose
Keypoint-MoSeq	Open source	Unsupervised behavioral syllable discovery from keypoints
VAME	Open source	Unsupervised behavioral motif discovery from pose
DeepOF	Open source	Behavioral analysis of DeepLabCut/SLEAP tracking
TREBA	Open source	Trajectory embeddings for behavior representation learning
MotionMapper	Open source	Unsupervised behavioral mapping from postural dynamics
MoSeq	Open source	Depth-video behavioral syllable segmentation

Object detection

Software	Type	Description
YOLO (Ultralytics)	Open source	Real-time object detection, segmentation, and pose framework
Detectron2	Open source	Object detection and instance segmentation library
Segment Anything (SAM 2)	Open source	Promptable image and video segmentation

Analysis and real-time pipelines

Software	Type	Description
DLC-Analyzer	Open source	Analysis and visualization of DeepLabCut output
DeepLabCut-Live	Open source	Real-time pose estimation on live video
DeepLabStream	Open source	Real-time, closed-loop pose-based feedback
Bonsai	Open source	Visual reactive programming for experiment pipelines
AMBER-pipeline	Open source	Automated rodent maternal-behavior analysis

Manual annotation

Software	Type	Description
BORIS	Open source	Event-logging and manual video annotation
Solomon Coder	Freeware	Manual behavior coding tool
Noldus Observer XT	Commercial	Manual behavior annotation suite
CVAT	Open source	Image and video annotation for detection, segmentation, and keypoints
Label Studio	Open source	Multi-type data labeling and annotation platform
VIA (VGG Image Annotator)	Open source	Lightweight image, audio, and video annotation tool
ELAN	Open source	Time-aligned annotation of video and audio

Commercial platforms

Software	Type	Description
Ethovision XT	Commercial	Video tracking and analysis
CatWalk XT	Commercial	Gait analysis platform