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  • Transforming Science at SRC with Nondestructive Synchrotron FTIR Spectro-Microtomography

    Chris Moore


    Researchers at the Synchrotron Radiation Center (SRC) have developed, for the first time, Fourier transform infrared spectro-microtomography.  This powerful technology allows for nondestructive three-dimensional imaging that reveals the distribution of distinctive chemistry throughout an intact biological or materials sample.  By yielding spectral data for each voxel of the 3D sample, it is now possible to easily characterize, for example, fragile cell structures throughout a cell body.  This work is reported in the Journal Nature Methods, and was the result of a collaboration between SRC Users Carol Hirschmugl from UW-Milwaukee and Michael Martin from Lawrence Berkeley National Laboratory.

    Carol Hirschmugl and Michael Martin

    Corresponding authors Carol Hirschmugl and Michael Martin at an SRC Users’ meeting.  (Photo by  Chris Moore, SRC)

    The development of this new technique was the result of a convergence of expertise and technology at SRC including rapid, high-quality, wide-field 2D infrared imaging at the microscale. The synchrotron light is critical, providing high signal to noise. The key to this technique is the existence of a unique instrument called the Infrared Environmental Imaging (IRENI) beamline at SRC.  Hirschmugl and SRC staff developed this high spatial-resolution infrared imaging instrument with funding from the National Science Foundation. 

    Hirschmugl says, “The critical components of IRENI for IR tomography experiments are that it collects 12 beams of synchrotron infrared light to homogeneously illuminate a 128 x 128 array detector (like a CCD camera for infrared) for which high quality spectral data is rapidly collected for every pixel in parallel.”  Spectral data, which are variations of the absorption of IR light for every wavelength, are used to determine the molecular structure of a sample.

    Hirschmugl and Martin applied existing computed tomography reconstruction methods (CT-scans) to frequency dependent data from the IRENI instrument yielding spectral information for every voxel.  A voxel is a 3D volume element, analogous to a pixel in 2D.  When carefully rotating a sample, 2D projections of spectrally rich data at many angles were collected. Millions of voxels of data containing  spectra data were extracted using CT reconstruction algorithms that were modified to evaluate all wavelengths, and this powerful new technology was born.

    3D IR Tomography Stage

    Test sample rotation stage at the SRC IRENI beamline used to take 3D IR Tomography data. (Photo by C. Hirschmugl, UW-M)

    The significance of this new technology cannot be overstated.  “Existing methods of studying the delicate structures within a cell include slicing, staining, chemically labeling, and adding contrast agents, techniques that modify cell structures in some way,” says Hirschmugl.  With this technique scientists can now study essential cell functions within living tissue including their architecture, mechanical movement, bioc20mical triggers, and cell-to-cell communication, all without affecting the living system under study. 

    In their journal publication, Hirschmugl and Martin showcased the measurement, 3D reconstruction, and composition of a single Zinnia elegans cell, a sliver from a fast-growing Populus tree, the internal structure and composition down the axis of a human hair, and the biochemical structure of a colony of mouse stem cells.  A better understanding of the structure and composition of cells like the Zinnia or the Populus tree is needed for making biofuels from cellulose.  Analysis of a human hair revealed a distinctive biochemical construction, including different distributions of material down the axis of the hair, while imaging the stem cell colony showed the ability of this technique to analyze in 3D crucial delicate structures impossible to study in any other way.

    Tomography of a Sliver of Populous Wood

    A sliver of populous wood (a), two 3-D reconstructions (b, c), and 3 cross sections (d– i).  The analysis and reconstruction, made possible by co-authors Barbara Illman and Julia Sedlmair from the Forest Products Laboratory, was done without destroying (cutting) the sample.

    Future work by Hirschmugl and Martin include plans to improve the efficiency of data collection and analysis and inclusion of advances in other fields to automate the collection, processing, and storage of large spectra tomographic data sets.  Additional improvements will also result from continued advances in mid-IR array detector technologies and synchrotron IR beamlines.  This new powerful method will facilitate a wide variety of scientific, industrial, materials, energy and medical applications ranging from understanding how to produce biofuels to the functioning of stem cells.

    Co-authors participating in this experiment provided expertise in tomographic reconstructions and samples of interest and sample preparation.  They include colleagues from Forest Products Laboratory (Barbara Illman, Julia Sedlmair), UW-Milwaukee (Miriam Unger), Lawrence Berkeley National Laboratory (Charlotte Dabat-Blondeau, Hans Bechtel, Dilworth Parkinson), University of Mainz (Jonathan Castro), Lawrence Livermore National Laboratory (Marco Keiluweit), University of UW-Madison (David Buschke, Brenda Ogle), and Karlsruhe Institute of Technology (Michael Nasse). 

    This research was funded by the DOE Office of Science and the National Science Foundation.  Berkeley Lab’s ALS and NERSC are funded by the DOE Office of Science.  SRC is primarily funded by the University of Wisconsin-Madison, with supplemental support from facility users and the University of Wisconsin-Milwaukee. 

    Additional Information:
    News release from Berkeley Lab

    Nature Methods Paper (a subscription may be required)

    For more information about IRENI and associated publications, please visit the IRENI page.


    The Synchrotron Radiation Center (SRC) of the University of Wisconsin-Madison is a national light source facility providing infrared, ultra violet, and soft X-ray light for use in research on exotic materials, ranging from high temperature superconductors and computer chips to cancer cells.  SRC provides an environment uniquely suited to the performance of seminal research, the development of new experimental techniques and instrumentation, and the training of scientists for the future.

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