Advances and challenges in cryo ptychography at the Advanced Photon Source

Abstract

Ptychography has emerged as a nondestructive tool to quantitatively study extended samples at a high spatial resolution. In this manuscript, we report on recent developments from our team. We have combined cryo ptychography and fluorescence microscopy to provide simultaneous views of ultrastructure and elemental composition, we have developed multi-GPU parallel computation to speed up ptychographic reconstructions, and we have implemented fly-scan ptychography to allow for faster data acquisition. We conclude with a discussion of future challenges in high-resolution 3D ptychography.

Keywords: 3D ptychography; cryogenic sample; fly scan; parallel computation; ptychography.

FIGURE 1

Simultaneous x-ray fluorescence and ptychographic imaging of a frozen-hydrated Chlamydomonas reinhardtii alga obtained from a 167×151 point scan data [14]. (a) X-ray fluorescence maps reveal the distribution of several elements in the alga. (b) The ptychographic reconstruction shows the biological ultrastructure at sub-30 nm resolution. The ptychographic image reveals features not seen in the elemental maps and adds rich contextual information. (c) Multiple-GPU parallel reconstruction. The 167×151 diffraction patterns were partitioned across several GPUs to reduce processing time from hours to minutes, after which the reconstruction results from each GPU are stitched together to form one image as shown in (b).

FIGURE 2

Fly-scan 3D ptychography on a gold test sample with a thickness of 200 nm. 31 projections of 40 × 30 scan points each were recorded in fly-scan mode with a 5.2 keV focused beam of ~100 nm, spanning a range of tilt angles from −60° to 60° with 4° angular spacing; the acquisition time per projection (covering 2 × 3 μm) is about 3 min with an exposure time of 110 ms per point, yielding the total collection time of ~1.5 hours for the whole 3D dataset. (a) Projection image reconstructed from ptychographic data at 0° using 5 probe modes. (b) 3D volume rendering of the tomographic reconstruction.

FIGURE 3

Depth of field (DOF; Eq. 1) as a function of the achieved transverse resolution at a series of photon energies. As the transverse resolution improves, the depth of field decreases with the square of these improvements, putting a limit on the sample thickness for straightforward interpretation. The red curve is the DOF limit at 6.2 keV, the energy of ptychographic tomography demonstrations (red dots; see [11, 27, 4, 28, 12, 29, 30, 31, 32]) at the cSAXS beamline at the Swiss Light Source routinely conduct the 3D ptychography. The blue dot represents our fly-scan 3D ptychography study (Fig. 2) at 5.2 keV.