Software, data and publications related to laboratory animal tracking.

* Not fulfilling all requirements of a true awesome list. Although many items on the list are truly awesome, I haven't tested all of them.

Deep learning powers a motion-tracking revolution, Nature, 2019.

ABCTracker: an easy-to-use, cloud-based application for tracking multiple objects, 2020. [paper] [website] #windows #closed_source

idtracker.ai: Tracking all individuals in large collectives of unmarked animals, 2018. [website] [paper] [code] #python

Tracktor: image-based automated tracking of animal movement and behaviour, 2018. [paper] [code] #python

ToxTrac: a fast and robust software for tracking organisms, 2018. [paper] [code] #windows

Pinpoint: behavioral tracking using 2D barcode tags, 2017. [code] #python

idTracker: Tracking individuals in a group by automatic identification of unmarked animals, 2014. [paper] [website] #matlab

Ilastik: Interactive learning and segmentation toolkit, 2011. [website] [paper] [code] #python

Ctrax: The Caltech Multiple Walking Fly Tracker, 2009. [paper] [website, code] #matlab

DeepLabCut: Multi-animal pose estimation and tracking with DeepLabCut, 2021. [website] [paper], [code] #python

SLEAP: Social LEAP Estimates Animal Poses, 2020. [website] [code] [paper] #python

DeepPoseKit, a software toolkit for fast and robust animal pose estimation using deep learning, 2019. [paper] [code] #python

DeepFly3D, motion capture (markerless 3D pose estimation) pipeline and helper GUI for tethered Drosophila, 2019. [paper] [code] #python

APT - The Animal Part Tracker, 2018. [website] [code] #matlab

Mice Behaviour Analysis Datasets

toxtrac

idtracker.ai

• 10, 60, 80, 100 zebrafish
• 38, 60, 72, 80, 100 flies

Zebrafish tracking using convolutional neural networks, 2017. https://www.nature.com/articles/srep42815, [video S1, video S2, video S3, video S4P1, video S4P2 low resolution 480x272 or 306x308]

idTracker: example video of 5 zebrafish

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