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3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography

Nature Methods volume 10, pages 861–864 (2013)Cite this article

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Abstract

We report Fourier transform infrared spectro-microtomography, a nondestructive three-dimensional imaging approach that reveals the distribution of distinctive chemical compositions throughout an intact biological or materials sample. The method combines mid-infrared absorption contrast with computed tomographic data acquisition and reconstruction to enhance chemical and morphological localization by determining a complete infrared spectrum for every voxel (millions of spectra determined per sample).

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Figure 1: FTIR spectro-microtomographic imaging of Zinnia.
Figure 2: Lignocellulose, hemicellulose and CH functional group distributions in a Populus wood fiber.
Figure 3: 2D and 3D chemical images of hair.
Figure 4: Top and side views of 3D protein and lipid distributions for an embryoid body colony of stem cells.

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Acknowledgements

Thanks to K. Krueger, M. Fisher and G. Rogers for outstanding machining skills and technical support. We also thank D. Ron for assistance on the spectral extractions. This work is based on research conducted at the IRENI beamline, whose construction and development was supported by the US National Science Foundation by award MRI-0619759. This work was supported by the US National Science Foundation under grant CHE-1112433. The ALS is supported by the Director, Office of Science, Office of Basic Energy Sciences, US Department of Energy under contract no. DE-AC02-05CH11231. The SRC is primarily funded by the University of Wisconsin–Madison, with supplemental support from facility users and the University of Wisconsin–Milwaukee.

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Author notes

  1. Charlotte Dabat-Blondeau & Miriam Unger

    Present address: Present addresses: Ecole Nationale Supérieure d'Ingénieurs de Caen, Caen, France (C.D.-B.); Cetics Healthcare Technologies GmbH, Esslingen am Neckar, Germany (M.U.).,

Authors and Affiliations

  1. Advanced Light Source Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

    Michael C Martin, Charlotte Dabat-Blondeau, Dilworth Y Parkinson & Hans A Bechtel

  2. Physics Department, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin, USA

    Miriam Unger & Carol J Hirschmugl

  3. US Department of Agriculture Forest Service, Forest Products Laboratory, Madison, Wisconsin, USA

    Julia Sedlmair & Barbara Illman

  4. Synchrotron Radiation Center, University of Wisconsin–Madison, Stoughton, Wisconsin, USA

    Julia Sedlmair & Barbara Illman

  5. Institute of Geosciences, University of Mainz, Mainz, Germany

    Jonathan M Castro

  6. Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA

    Marco Keiluweit

  7. Department of Biomedical Engineering, University of Wisconsin–Madison, Madison, Wisconsin, USA

    David Buschke & Brenda Ogle

  8. Laboratory for Applications of Synchrotron Radiation, Karlsruhe Institute of Technology, Karlsruhe, Germany

    Michael J Nasse

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Contributions

M.C.M. and C.J.H. conceived of the technique and led the project. C.D.-B. wrote automated data analysis code and carried out some of the experiments. M.J.N. wrote scripts to automate the data collection at IRENI. M.U. and J.S. helped perform all experiments. D.Y.P. provided tomographic reconstruction algorithms and expert advice on setting up the experiments. H.A.B. provided optical mount expertise and assistance with analysis codes. B.I. provided Populus samples and helped perform experiments and analysis of these samples. J.M.C. provided the volcanic samples and expertise for their analysis. M.K. provided the Zinnia samples and expertise for their analysis. D.B. and B.O. provided embryoid body colony samples and expertise for their analysis. All authors helped with writing this paper.

Corresponding authors

Correspondence to Michael C Martin or Carol J Hirschmugl.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Note (PDF 698 kb)

Tomographic reconstruction of a Zinnia elegans tracheary element inside a polyimide microloop holder shown in Figure 1

The red color shows the reconstruction of the integrated intensity from the 2356.7–2376.0 cm−1 spectral region, where only the sharp edges of the microloop are visualized. After a little time, the blue-green colors are turned on that show the reconstruction of the 3317–3340 cm−1 spectral region associated with O-H stretching. The parallel secondary cell wall thickenings of the Zinnia elegans are now clearly visualized. (MOV 331 kb)

3D reconstruction of a Populus wood sample in Figure 2, shown rotating

The brown colors are reconstructed intensities of hydrocarbon stretching absorption modes in the 2804–3023 cm−1 spectral range. The blue-green colors are associated with holocellulose (1689–1781 cm−1). (MOV 1769 kb)

Movie of the full tomographic reconstructions obtained from an intact human hair from Figure 3 showing absorptions of protein (red) and phospholipid (blue-green)

The medulla is observed to have little protein as we see the protein reconstruction is indeed hollow, but it instead has higher concentrations of phospholipids. (MOV 620 kb)

Movie of the full tomographic reconstructions obtained from mouse stem cells from Figure 4 showing absorptions of protein (blue-red) and lipids (yellow-brown)

The movie starts showing on the protein distribution, then the lipids turn on and we see the overlapping distributions, and finally the proteins turn off to show the lipid distribution. (MOV 2990 kb)

Video showing the tomographic reconstruction of the integrated absorption in the 1573–1654 cm−1 spectral range for a polyimide microloop

Static images from this movie are shown in the top row of Supplementary Figure 2. (MOV 722 kb)

Video of the reconstructed volcanic glass sample shown in Supplementary Figures 4 and 5

The red-brown colors show the 1790 cm−1 absorptive regions, and the blue-green colors are the 3494 cm−1 absorptive regions superimposed on each other. The blue-green is dominated by water absorptions, (due to the combined H2O and OH stretching vibrations), whereas the red-brown regions are predominately the edge of the strong silicate glass absorption. The white space between has low absorbance at both spectral regions. (MOV 1102 kb)

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Martin, M., Dabat-Blondeau, C., Unger, M. et al. 3D spectral imaging with synchrotron Fourier transform infrared spectro-microtomography. Nat Methods 10, 861–864 (2013). https://doi.org/10.1038/nmeth.2596

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