Dataset Information

Integrating XMALab and DeepLabCut for high-throughput XROMM.

ABSTRACT: Marker tracking is a major bottleneck in studies involving X-ray reconstruction of moving morphology (XROMM). Here, we tested whether DeepLabCut, a new deep learning package built for markerless tracking, could be applied to videoradiographic data to improve data processing throughput. Our novel workflow integrates XMALab, the existing XROMM marker tracking software, and DeepLabCut while retaining each program's utility. XMALab is used for generating training datasets, error correction and 3D reconstruction, whereas the majority of marker tracking is transferred to DeepLabCut for automatic batch processing. In the two case studies that involved an in vivo behavior, our workflow achieved a 6 to 13-fold increase in data throughput. In the third case study, which involved an acyclic, post-mortem manipulation, DeepLabCut struggled to generalize to the range of novel poses and did not surpass the throughput of XMALab alone. Deployed in the proper context, this new workflow facilitates large scale XROMM studies that were previously precluded by software constraints.

SUBMITTER: Laurence-Chasen JD

PROVIDER: S-EPMC7490514 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Integrating XMALab and DeepLabCut for high-throughput XROMM.

Laurence-Chasen J D JD Manafzadeh Armita R AR Hatsopoulos Nicholas G NG Ross Callum F CF Arce-McShane Fritzie I FI

The Journal of experimental biology 20200904 Pt 17

Marker tracking is a major bottleneck in studies involving X-ray reconstruction of moving morphology (XROMM). Here, we tested whether DeepLabCut, a new deep learning package built for markerless tracking, could be applied to videoradiographic data to improve data processing throughput. Our novel workflow integrates XMALab, the existing XROMM marker tracking software, and DeepLabCut while retaining each program's utility. XMALab is used for generating training datasets, error correction and 3D re ...[more]

PMID: 32665442

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Dataset Information

Integrating XMALab and DeepLabCut for high-throughput XROMM.

Publications

Integrating XMALab and DeepLabCut for high-throughput XROMM.

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