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Research Spending & Results

Award Detail

Awardee:BROWN UNIVERSITY IN PROVIDENCE IN THE STATE OF RHODE ISLAND AND PROVIDENCE PLANTATIONS
Doing Business As Name:Brown University
PD/PI:
  • Elizabeth L Brainerd
  • (401) 863-9261
  • elizabeth_brainerd@brown.edu
Co-PD(s)/co-PI(s):
  • Stephen M Gatesy
Award Date:02/20/2013
Estimated Total Award Amount: $ 906,192
Funds Obligated to Date: $ 906,192
  • FY 2015=$312,086
  • FY 2014=$300,427
  • FY 2013=$293,679
Start Date:07/01/2013
End Date:06/30/2017
Transaction Type:Grant
Agency:NSF
Awarding Agency Code:4900
Funding Agency Code:4900
CFDA Number:47.074
Primary Program Source:040100 NSF RESEARCH & RELATED ACTIVIT
Award Title or Description:Collaborative Research: ABI Development: Integrated X-Ray Motion Analysis Software and Video Data Management for the Comparative Biomechanics Community
Federal Award ID Number:1262156
DUNS ID:001785542
Parent DUNS ID:001785542
Program:ADVANCES IN BIO INFORMATICS
Program Officer:
  • Jennifer Weller
  • (703) 292-8470
  • jweller@nsf.gov

Awardee Location

Street:BOX 1929
City:Providence
State:RI
ZIP:02912-9002
County:Providence
Country:US
Awardee Cong. District:01

Primary Place of Performance

Organization Name:Brown University
Street:BOX 1929
City:Providence
State:RI
ZIP:02912-1929
Country:US

Abstract at Time of Award

X-ray Reconstruction of Moving Morphology (XROMM) is a new technology for visualizing bones and joints during rapid motion, such as birds in flight, frogs jumping, and humans running. XROMM has already transformed studies of vertebrate animal motion, but the current software available for XROMM analysis is cumbersome and poorly integrated with data pipelines. This project will apply best practices of software engineering to create an open-source XROMM analysis package that is integrated with an online data management system. The software products will improve user experience, speed, robustness, and reproducibility of the XROMM analysis process. The low throughput of current tools is a problem because a fundamental goal of comparative biomechanics is to compare species, and thereby to extract robust relationships between form and function. The new tools developed through this award will significantly increase the throughput of the XROMM process, and also provide integrated analysis and management of complex data sets. This project will substantially enhance the cyberinfrastructure for comparative biomechanics research, and increase US economic competitiveness through technology development and advanced training of the scientific workforce. All software products and documentation will be open source and made freely available, and all source code will be deposited in a public code repository. Undergraduate and graduate students at Brown University, and undergraduates at Providence College (a primarily undergraduate institution), will gain interdisciplinary training in biology, engineering, and computer science. As part of this project, at least 45 students, researchers, and educators will participate in XROMM Short Courses at Brown (15 per year for 3 years). The XROMM Short Courses at Brown are an effective way to teach complex XROMM methods to researchers and educators at a range of career levels and from diverse types of institutions, including schools, colleges, and museums as well as research universities. All products from this project will be made available through www.xromm.org.

Publications Produced as a Result of this Research

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Camp, A.L., Astley, H.C., Horner, A. M., Roberts, T.J. and Brainerd, E.L. "Fluoromicrometry: a method for measuring muscle length dynamics with biplanar videofluoroscopy" Journal of Experimental Zoology, Part A, v., 2016, p.. doi:10.1002/jez.2031 

Kambic, R.E., Roberts, T.J. and Gatesy, S.M. "3?D range of motion envelopes reveal interacting degrees of freedom in avian hind limb joints" Journal of Anatomy, v., 2017, p.. doi:10.1111/joa.12680 

Menegaz, R.A., Baier, D.B., Metzger, K.A., Herring, S.W. and Brainerd, E.L. "XROMM analysis of tooth occlusion and temporomandibular joint kinematics during feeding in juvenile miniature pigs" Journal of Experimental Biology, v.218, 2015, p.. doi:10.1242/jeb.119438 

Brainerd, E.L, Moritz, S., and Ritter, D.A. "XROMM analysis of rib kinematics during lung ventilation in the green iguana, Iguana iguana" Journal of Experimental Biology, v.219, 2016, p.404. doi:doi: 10.1242/jeb.127928 

Kambic, R.E., Roberts, T.J. and Gatesy, S.M. "Guineafowl with a twist: asymmetric limb control in steady bipedal locomotion" Journal of Experimental Biology, v.218, 2015, p.3836. doi:10.1242/jeb.126193 

Kno?rlein, B.J., D.B. Baier, S.M. Gatesy, J.D. Laurence Chasen and E.L. Brainerd "Validation of XMALab Software for Marker-based XROMM" Journal of Experimental Biology, v., 2016, p.3701. doi:10.1242/jeb.145383 

Brainerd, E.L., Blob, R.W., Hedrick, T.L., Creamer, A.T. and Müller, U.K. "Data management rubric for video data in organismal biology" Integrative and Comparative Biology, v.57, 2017, p.33. doi:10.1093/icb/icx060 

Brocklehurst, R. J., Moritz, S., Codd, J., Sellers, W. I. and Brainerd, E. L. "Rib kinematics during lung ventilation in the American alligator (Alligator mississippiensis): an XROMM analysis" Journal of Experimental Biology, v.220, 2017, p.3181. doi:10.1242/jeb.156166 

Kambic, R.E., Roberts, T.J., Gatesy, S.M. "Long-axis rotation: a missing degree of freedom in avian bipedal locomotion" Journal of Experimental Biology, v.217, 2015, p.2770. doi:10.1242/jeb.101428 

Mayerl, C.J., Brainerd, E.L. and Blob, R.W. "Pelvic girdle mobility of cryptodire and pleurodire turtles during walking and swimming" Journal of Experimental Biology, v., 2016, p.2650. doi:10.1242/jeb.141622 

Gidmark, N.J., Taylor, C., LoPresti, E. and Brainerd, E.L. "Functional morphology of durophagy in black carp, Mylopharyngodon piceus" Journal of Morphology, v.276, 2015, p.1422. doi:10.1002/jmor.20430 

Camp, A.L. and Brainerd, E.L. "Reevaluating musculoskeletal linkages in suction-feeding fishes with X-Ray Reconstruction of Moving Morphology (XROMM)" Integrative and Comparative Biology, v.55, 2015, p.1. doi:10.1093/icb/icv034 

Camp, A.L., Roberts, T.J. and Brainerd, E.L. "Swimming muscles power suction feeding in largemouth bass" Proceedings of the National Academy of Sciences, v.112, 2015, p.8690. doi:10.1073/pnas.1508055112 

Allen, V.R., Kambic, R.E., Gatesy, S.M. and Hutchinson, J.R. "Gearing effects of the patella (knee extensor muscle sesamoid) of the helmeted guineafowl during terrestrial locomotion" Journal of Zoology, v., 2017, p.. doi:10.1111/jzo.12485 


Project Outcomes Report

Disclaimer

This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.

X-ray Reconstruction of Moving Morphology (XROMM) is a recently-developed technology for visualizing bones and joints in motion. XROMM combines 3D models of bone morphology with movement data from biplanar x-ray video to create highly accurate (±0.1 mm) animations of 3D bones moving in 3D space. XROMM adds fundamental new capabilities to the research toolkit for biomechanics, particularly the ability to measure 3D bone motion of the skeleton. For example, we can visualize the skeleton of a bird walking (see Figure 1 and http://www.xromm.org/).

Through this project we have developed a suite of open-source software tools for X-ray video data management, X-ray motion analysis, and XROMM animation. These tools have improved the user experience, speed, robustness, and reproducibility of the XROMM analysis process. The tools for managing data are online systems for video data management, the X-ray Motion Analysis Portal (http://xmaportal.org/) and the Zoological Motion Analysis Portal (http://zmaportal.org/). The motion analysis software is the X-ray Motion Analysis Lab (XMALab, https://bitbucket.org/xromm/xmalab). All resources developed through this award are open source and free on the web.

The greatest innovation of this project was integrating the online data management tools (XMAPortal and ZMAPortal) and the analysis tool (XMALab). Now researchers working with complex, 3D video data sets can keep all their data organized in the Portals, export to the analysis tool, do the analysis and then re-import the analyzed data back into the database. This workflow both increases the efficiency and pace of science and increases the reproducibility of results.

Together these tools contribute to the informatics infrastructure available for researchers and enhance US innovation and economic competitiveness.

 

 


Last Modified: 10/09/2017
Modified by: Elizabeth L Brainerd

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