Coded Aperture X-ray Microscopy

Coded Aperture X-ray Microscopy

We are developing a class of X-ray imaging methods that extract three-dimensional structural information without requiring physical movement of the sample. This work responds to longstanding challenges in diffraction-based imaging, including: 

  • Alignment sensitivity during rotation-based tomography
  • Mechanical instability in scanning systems
  • Limited access in in situ, high-pressure, or cryogenic environments

Background and Development

Our research has followed a stepwise progression, adapting coded aperture techniques to several imaging modalities:

  • Laue Microdiffraction: We began by scanning binary-coded masks across the diffracted beam to retrieve depth-resolved diffraction patterns. This provided a practical alternative to scanning wires or slits and allowed depth sensitivity in stationary samples.
  • Dark-field X-ray Microscopy: Structured illumination was introduced by modulating the incident beam with microfabricated coded apertures. This enabled 3D imaging without sample rotation or rastering.
  • Coherent Encoding: With the increased coherence from the upgraded APS source, we began integrating phase modulation with amplitude encoding. Simulations suggest improved spatial resolution, which may enhance sensitivity to strain and orientation variations.
  • Nano-holotomography: A single-distance scheme was developed for phase-contrast imaging. By scanning the aperture rather than moving the sample, this method simplifies data collection and supports time-resolved studies.
  • Grazing-Incidence Scattering: Structured illumination was adapted to surface-sensitive geometries. This approach extracts local structural variations across the beam footprint without relying on sample rotation.
  • Time-Coded Exposure: Introduced pseudo-random binary gating of detectors or shutters to recover usable data from motion-blurred tomographic scans.
  • Coded Illumination for Ptychography: Showed that modified uniformly redundant arrays can diimprove ptychographic resolution and convergence by enhancing far-field SNR.

Supporting Tools and Infrastructure 

  • Digital Autofocusing: To improve experimental reliability, we implemented a method for estimating coded aperture geometry directly from collected data. This avoids the need for external metrology or high-precision stages.
  • Microfabrication at CNM: All coded apertures used in these studies were fabricated at the Center for Nanoscale Materials (CNM), allowing rapid prototyping and fine-scale control over aperture design.
  • COLD Software Package: Python-based tool for reconstructing depth-resolved Laue signals from coded aperture scans. Supports raster and continuous scan modes, geometry calibration, and parallel processing.
  • CodEx Reconstruction Framework: Combined coded acquisition with ADMM-based joint deblurring and tomographic inversion, enabling accurate reconstructions from sparse, blurred views.
  • Cross-Facility HPC Processing: Real-time data transfer from APS to ALCF enables GPU-accelerated reconstruction on Polaris. Handles large scans within minutes during live experiments.

Alignment with APS Upgrade

These methods were designed with the capabilities of next-generation synchrotron sources in mind. The upgraded APS provides: 

  • Higher coherent flux for high-resolution imaging
  • Higher brightness for high-speed imaging
  • Greater compatibility with dynamic or constrained sample environments 

By keeping the sample stationary and structuring the beam instead, these approaches improve imaging speed, reduce mechanical overhead, and make advanced 3D imaging feasible under a wider range of conditions.

References

  • Gürsoy D, Sheyfer D, Wojcik M, Liu W, Tischler J. Optimizing Coded-Apertures for Depth-Resolved Diffraction. arXiv preprint arXiv:2405.12813. 2024.
  • Gürsoy D, Yay KA, Kisiel E, Wojcik M, Sheyfer D, Last A, Highland M, Fisher IR, Hruszkewycz S, Islam Z. Dark-field X-ray Microscopy with Structured Illumination for Three-Dimensional Imaging. Communications Physics. 2025;8(1):34.
  • Gürsoy D, Hruszkewycz S, Towards Dark-Field X-ray Microscopy through Coherent Encoding, IEEE ICIP (2023)
  • Nikitin V, Carlsson M, Mokso R, Cloetens P, Gürsoy D. Single-Distance Nano-Holotomography with Coded Apertures. Optics Letters. 2025 Jan 13;50(2):574-7.
  • Gürsoy D, Yang X, Sheyfer D, Wojcik M, Li R, Tsai E. Structured Illumination for Surface-Resolved Grazing-Incidence X-ray Scattering. arXiv preprint arXiv:2505.04803. 2025.
  • Gürsoy D, Sheyfer D, Wojcik M, Liu W, Tischler J. Digital Autofocusing of a Coded-Aperture Laue Diffraction Microscope. Review of Scientific Instruments. 2023;94(1).
  • Prince M, Gürsoy D, Sheyfer D, Chard R, Côté B, Parraga H, Frosik B, Tischler J, Schwarz N. Demonstrating Cross-Facility Data Processing at Scale with Laue Microdiffraction. Proceedings of the SC'23 Workshops (pp. 2133-2139).
  • Ching D, Aslan S, Nikitin V, Gürsoy D. Time-Coded Aperture for X-ray Imaging. Optics Letters. 2019;44(11):2803-6.
  • Ching DJ, Aslan S, Nikitin V, Wojcik MJ, Gursoy D. Evaluation of modified uniformly redundant arrays as structured illuminations for ptychography. arXiv preprint arXiv:2004.01766. 2020.
  • Majee S, Aslan S, Gürsoy D, Bouman CA. CodEx: a Modular Framework for Joint Temporal Deblurring and Tomographic Reconstruction. IEEE Transactions on Computational Imaging. 2022;8:666-78.