[Paper Review] Microtomography on the ANATOMIX beamline at Synchrotron SOLEIL

T. Weitkamp, M. Scheel+17 more|arXiv (Cornell University)|Feb 8, 2020

Advanced X-ray Imaging Techniques4 citations

TL;DR

This paper presents the ANATOMIX beamline at Synchrotron SOLEIL, dedicated to hard X-ray full-field microtomography and nanotomography with photon energies from 5 to 50 keV. It enables high-resolution imaging from 20 nm to 20 µm using absorption and phase-contrast techniques, supporting large samples up to 40 mm wide via variable beam optics and advanced detectors, with applications in materials science, biomedicine, and in-situ studies.

ABSTRACT

The ANATOMIX beamline at Synchrotron SOLEIL, operational since 2018, is dedicated to hard X-ray full-field tomography techniques. Operating in a range of photon energies from approximately 5 to 50 keV, it offers both parallel-beam projection microtomography, in absorption and phase contrast, and nanotomography using a zone-plate transmission X-ray microscope. With these methods, the beamline covers a range of spatial resolution from 20 nm to 20 $μ$m, expressed in terms of useful pixel size. The variable beam size of up to 40 mm allows users to image large objects. Here we describe the microtomography instrumentation of the beamline.

Motivation & Objective

• To develop a dedicated hard X-ray microtomography beamline at SOLEIL for high-resolution 3D imaging of diverse materials and biological samples.
• To provide both absorption and phase-contrast imaging modes to enhance visibility of low-absorbing or soft materials.
• To support large samples (up to 40 mm wide) through variable beam focusing and extended propagation distances up to 37 m.
• To enable in-situ and time-resolved studies using fast rotation stages and high-speed detectors.
• To integrate advanced detector optics and reconstruction pipelines for efficient, high-fidelity 3D imaging across multiple length scales.

Proposed method

• Utilizes a long undulator source (U18) with in-vacuum, cryogenically cooled operation to deliver high-brightness X-rays.
• Employs a double-crystal Si-111 monochromator (DCM) and future double-multilayer monochromator for energy selection between 7–50 keV.
• Applies horizontally focusing beryllium mirrors and refractive lenses to control beam size and flux density at the sample.
• Employs multiple detector optics (0.48× to 20× magnification) and high-speed cameras (up to 2277 fps) for variable spatial resolution.
• Uses on-the-fly rotation stages (RT500S and RT150S) with synchronization via the Flyscan architecture for rapid tomography.
• Applies Paganin filter and PyHST2 reconstruction software on a local 5-node cluster for fast, high-quality 3D volume reconstruction.

Experimental results

Research questions

• RQ1 How can hard X-ray microtomography achieve high spatial resolution (down to 20 nm) while maintaining large field-of-view capabilities?
• RQ2 What are the optimal configurations for phase-contrast imaging in microtomography to enhance soft-tissue and low-absorption contrast?
• RQ3 How can beamline design support both standard and ultrafast tomography (up to 20 scans per second) for dynamic processes?
• RQ4 What are the performance limits of full-field tomography using filtered white beams and monochromatic beams across different sample sizes?
• RQ5 How can the integration of micro- and nanotomography stations enable correlative imaging in a single experimental session?

Key findings

• The ANATOMIX beamline achieves a minimum effective pixel size of 20 nm in nanotomography and 130 nm in microtomography, enabling multi-scale imaging.
• Phase-contrast microtomography with a 6.5 µm pixel size successfully visualized muscle tissue in a 37 mm-long wall lizard head in just 7 minutes.
• A 325 nm pixel size microtomography scan of an Arabidopsis thaliana seed resolved protein storage vacuoles in a 0.3 mm diameter sample.
• The beamline supports up to 20 tomography scans per second using the RT150S fast rotation stage and high-speed pco.dimax HS4 camera.
• A 2048³ voxel tomographic volume is reconstructed in approximately 3 minutes using PyHST2 on a 5-node computing cluster.
• The beamline enables coupled micro- and nanotomography experiments, as demonstrated by correlative imaging of the same sample in a single session.