Abstract
High-speed X-ray diffraction is the state-of-the-art approach to understanding protein structure and dynamics in living tissues, especially muscles. Existing analytic approaches, however, require expert hand-digitization to extract parameters of interest. This produces repeatable measurements, but remains subjective and does not offer information on the precision of the measured parameters or strict reproducibility of analyzed data. We developed a processing tool chain, which first segments the diffraction image into regions of interest using highly conserved features and then samples the possible parameter values with a Markov chain Monte Carlo approach. Our approach produces an automated, reproducible, objective estimate of relevant image parameters.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Bagni, M.A., Cecchi, G., Griffiths, P.J., Maeda, Y., Rapp, G., Ashley, C.C.: Lattice spacing changes accompanying isometric tension development in intact single muscle fibers. Biophys. J. 67(5), 1965–1975 (1994)
Bradski, G.: OpenCV: an open source computer vision library. Dr. Dobb’s J. Softw. Tools (2000)
Brenner, B., Yu, L.C.: Equatorial x-ray diffraction from single skinned rabbit psoas fibers at various degrees of activation. Changes in intensities and lattice spacing. Biophys. J. 48(5), 829–834 (1985)
Foreman-Mackey, D., Hogg, D.W., Lang, D., Goodman, J.: emcee: The MCMC hammer. PASP 125(925), 306–312 (2013)
George, N.T., Irving, T.C., Williams, C.D., Daniel, T.L.: The cross-bridge spring: can cool muscles store elastic energy? Science 340(6137), 1217–1220 (2013)
Irving, T.C.: X-ray diffraction of indirect flight muscle from drosophila in vivo. In: Vigoreaux, J.O. (ed.) Nature’s Versatile Engine: Insect Flight Muscle Inside and Out, Landes Bioscience, Georgetown, TX, pp. 197–213 (2006)
Jnr, M.M.H., Veeraraghavan, V.G., Rubin, H., Winchell, P.G.: The approximation of symmetric x-ray peaks by pearson type vii distributions. J. Appl. Cryst. 10, 66–68 (1977)
Millman, B.M.: The filament lattice of striated muscle. Physiol Rev. 78(2), 359–391 (1998)
Reedy, M.K., Holmes, K.C., Tregear, R.T.: Induced changes in orientation of the cross-bridges of glycerinated insect flight muscle. Nature 207(5003), 1276–1280 (1965)
Williams, C.D., Salcedo, M.K., Irving, T.C., Regnier, M., Daniel, T.L.: The length-tension curve in muscle depends on lattice spacing. Proc. Biol. Sci. 280(1766), 20130697 (2013)
Acknowledgments
This work was supported in part by NSF grant IIS-1110370, the Intel Science and Technology Center for Big Data, the Army Research Office through ARO Grants W911NF-13-1-0435 and W911NF-14-1-0396, an award from the Gordon and Betty Moore Foundation and the Alfred P Sloan Foundation, the Washington Research Foundation Fund for Innovation in Data-Intensive Discovery, and the UW eScience Institute.
We thank Jake VanderPlas for helpful discussions of statistical techniques, Tom Irving for advice on X-ray imaging, Gideon Dunster for digitization of diffraction images, and Simon Sponberg for the sharing of diffraction images.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2016 Springer International Publishing Switzerland
About this paper
Cite this paper
Williams, C.D., Balazinska, M., Daniel, T.L. (2016). Automated Analysis of Muscle X-ray Diffraction Imaging with MCMC. In: Wang, F., Luo, G., Weng, C., Khan, A., Mitra, P., Yu, C. (eds) Biomedical Data Management and Graph Online Querying. Big-O(Q) DMAH 2015 2015. Lecture Notes in Computer Science(), vol 9579. Springer, Cham. https://doi.org/10.1007/978-3-319-41576-5_9
Download citation
DOI: https://doi.org/10.1007/978-3-319-41576-5_9
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-41575-8
Online ISBN: 978-3-319-41576-5
eBook Packages: Computer ScienceComputer Science (R0)