Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


Title: CoralCT : A platform for transparent and collaborative analyses of growth parameters in coral skeletal cores
Abstract We present CoralCT, a software application for analysis of annual extension, density, and calcification in coral skeletal cores. CoralCT can be used to analyze computed tomography (CT) scans or X‐ray images of skeletal cores through a process in which observers interact with images of a core to define the locations of annual density bands. The application streamlines this process by organizing the observer‐defined banding patterns and automatically measuring growth parameters. Analyses can be conducted in two or three dimensions, and observers have the option to utilize an automatic band‐detection feature. CoralCT is linked to a server that stores the raw CT and X‐ray image data, as well as output growth rate data for hundreds of cores. Overall, this server‐based system enables broad collaborations on coral core analysis with standardized methods and—crucially—creates a pathway for implementing multiobserver analysis. We assess the method by comparing multiple techniques for measuring annual extension and density, including a corallite‐tracing approach, medical imaging software, two‐dimensional vs. three‐dimensional analyses, and between multiple observers. We recommend that CoralCT be used not only as a measurement tool but also as a platform for data archiving and conducting open, collaborative science.  more » « less
Award ID(s):
2444864
PAR ID:
10581070
Author(s) / Creator(s):
; ; ; ; ; ;
Publisher / Repository:
Limnology and Oceanography Methods
Date Published:
Journal Name:
Limnology and Oceanography: Methods
Volume:
23
Issue:
2
ISSN:
1541-5856
Page Range / eLocation ID:
97 to 116
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; ; ; ; et al (, Earth System Science Data)
    Abstract. As science fields enter the Big Data revolution, open-access repositories are essential for addressing larger-scale questions than are possible for single researchers by making data findable, accessible, interoperable, and reusable (FAIR). Furthermore, transparent data and code are increasingly important for reproducible research, especially for data types that inherently require subjective human interpretations. These ideas are applicable to coral sclerochronology, as the field has long been characterized by individual researchers collecting and analyzing coral skeletal cores from their study sites without substantial data sharing or archiving of the core images to meet FAIR principles. Here, we present CoralCache, a virtual coral core repository that not only archives image datasets (i.e., digitized X-rays and computed tomography scans), but also observer interpretations of the density banding patterns. CoralCache is linked to a graphical user interface, CoralCT, which together offer a way forward for coral growth rate analysis that is reproducible and collaborative. The data organization systems presented here could also be readily applied to related archives such as tree rings or bivalve shells. 
    more » « less
  2. ; ; ; ; ; ; ; ; ; ; et al (, Earth system science data)
    As science fields enter the Big Data revolution, open-access repositories are essential for addressing larger-scale questions than are possible for single researchers by making data findable, accessible, interoperable, and reusable (FAIR). Furthermore, transparent data and code are increasingly important for reproducible research, especially for data types that inherently require subjective human interpretations. These ideas are applicable to coral sclerochronology, as the field has long been characterized by individual researchers collecting and analyzing coral skeletal cores from their study sites without substantial data sharing or archiving of the core images to meet FAIR principles. Here, we present CoralCache, a virtual coral core repository that not only archives image datasets (i.e., digitized X-rays and computed tomography scans), but also observer interpretations of the density banding patterns. CoralCache is linked to a graphical user interface, CoralCT, which together offer a way forward for coral growth rate analysis that is reproducible and collaborative. The data organization systems presented here could also be readily applied to related archives such as tree rings or bivalve shells. 
    more » « less
  3. ; ; (, Protocolsio)
    Coral morphology is influenced by genetics, the environment, or the interaction of both, and thus is highly variable. This protocol outlines a non-destructive and relatively simple method for measuring Scleractinian coral subcorallite skeletal structures (such as the septa length, theca thickness, and corallite diameter, etc.) using digital images produced as a result of digital microscopy or from scanning electron microscopy. This method uses X and Y coordinates of points placed onto photomicrographs to automatically calculate the length and/or diameter of a variety of sub-corallite skeletal structures in the Scleractinian coral Porites lobata. However, this protocol can be easily adapted for other coral species - the only difference may be the specific skeletal structures that are measured (for example, not all coral species have a pronounced columella or pali, or even circular corallites). This protocol is adapted from the methods described in Forsman et al. (2015) & Tisthammer et al. (2018). There are 4 steps to this protocol: 1) Removal of Organic Tissue from Coral Skeletons 2) Imaging of Coral Skeletons 3) Photomicrograph Image Analysis 4) Calculation of Corallite Microstructure Size dx.doi.org/10.17504/protocols.io.bx5bpq2n 
    more » « less
  4. ; ; ; ; ; ; ; (, Protein Science)
    Abstract New X‐ray crystallography and cryo‐electron microscopy (cryo‐EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open‐source under the MIT license, and is available athttps://github.com/ExcitedStates/qfit-3.0. 
    more » « less
  5. ; ; ; ; ; ; ; ; ; ; et al (, The Astrophysical Journal)
    Abstract We perform X-ray spectral analyses to derive the characteristics (e.g., column density, X-ray luminosity) of ≈10,200 active galactic nuclei (AGNs) in the XMM-Spitzer Extragalactic Representative Volume Survey, which was designed to investigate the growth of supermassive black holes across a wide dynamic range of cosmic environments. Using physical torus models (e.g., Borus02) and a Bayesian approach, we uncover 22 representative Compton-thick (CT; N H > 1.5 × 10 24 cm −2 ) AGN candidates with good signal-to-noise ratios as well as a large sample of 136 heavily obscured AGNs. We also find an increasing CT fraction ( f CT ) from low ( z < 0.75) to high ( z > 0.75) redshift. Our CT candidates tend to show hard X-ray spectral shapes and dust extinction in their spectral energy distribution fits, which may shed light on the connection between AGN obscuration and host-galaxy evolution. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Text Encoded Conversion
  • XML
  • Save / Share this Record
  • Send to Email