Calendar of Events

Speaker: Viktor Nikitin, Assistant Physicist, X-Ray Science Division, Argonne National Laboratory

Title:  TomocuPy: a GPU Alternative to TomoPy

Date:    January 30, 2023

  Time:  1:00 p.m. (Central Time)

Location:

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https://argonne.zoomgov.com/j/1610942256?pwd=MVlISit5b1JURzN4TjVUc0dDQStzQT09

Meeting ID: 161 094 2256
Passcode: 748529
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Meeting ID: 161 094 2256

Abstract:

Real-time 3D data analysis and steering of a dynamic tomographic experiment by changing environmental conditions or acquisition parameters require fast, close to real-time, 3D reconstruction of large data volumes. Here we present a performance-optimized TomocuPy package as a GPU alternative to the commonly used CPU-based TomoPy package for tomographic reconstruction. TomocuPy utilizes modern hardware capabilities to organize a fast 3D reconstruction conveyor involving parallel read-write operations with storage drives, CPU-GPU data transfers, and GPU computations. In the conveyor, all the operations are timely overlapped to almost fully hide all data management time. Since most cameras work with less than 16-bit digital output, we furthermore optimize the memory usage and processing speed by using 16-bit floating-point arithmetic. As a result, 3D reconstruction with TomocuPy became 20-30 times faster than its multithreaded CPU equivalent. Full reconstruction (including read-write operations and methods initialization) of a 2048×20482048 tomographic volume takes less than 7 s on a single Nvidia Tesla A100 and PCIe 4.0 NVMe SSD, and scales almost linearly increasing the data size. To simplify operation at synchrotron beamlines, TomocuPy provides an easy-to-use command-line interface. The efficacy of the package was demonstrated during a tomographic experiment on gas-hydrate formation in porous samples, where a steering option was implemented as a lens-changing mechanism for zooming to regions of interest.

CAMERA Seminar

Title: The Multi-Tiered Iterative Projection Framework: How to exploit the mathematical structure of inverse problems to reconstruct complex structure from challenging experimental data

Speaker: Jeffrey Donatelli, CAMERA, Lawrence Berkeley National Laboratory

Date: Tuesday, January 31, 2023

Time: Noon Central Time | 10:00 AM Pacific Time

Location:

Zoom link available day before at https://camera.lbl.gov/seminars.

Abstract:

New experimental technologies have the potential to capture information from important biological objects and new materials at unprecedented detail and scales. However, the accelerating size, rate, complexity, and sensitivity of these new measurements are far outpacing the capability of traditional inversion methods to efficiently and robustly reconstruct the desired information from the data. In this talk, I will present a new general mathematical framework capable of overcoming many of these challenges in inversion. This framework, called Multi- Tiered Iterative Projections (M-TIP), is based on exploiting the mathematical structure of the inverse problem via an iterative application of projection operators that optimally target the physics of the experiment to maximize speed, accuracy, and robustness. I will demonstrate the use of M-TIP in solving important open problems in inversion from fluctuation scattering, single-particle diffraction, coherent surface scattering imaging, multiple-scattering electron crystallography, and more.

Director’s Special Colloquium

Friday, Feb. 3, 2023, 10 – 11:30 a.m. CT
Live in Building 241
Room D172

Nipam H. Patel, director of the Marine Biological Laboratory and professor at the University of Chicago, will present  ​“Learning from Nature: Bioinspired Nanomaterials via Bioinspired Fabrication” at a Director’s Special Colloquium. All employees are invited to attend.
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Abstract:
Evolution has already come up with the solution to many of our problems – our challenge is to identify the organisms that hold the answers to these questions, and also develop the tools to understand these solutions in sufficient detail to make use of them to solve the obstacles we face. A clear example of this comes from bioinspired materials, such as ultra-strong fibers that mimic spider silk, or sticky surfaces that are modeled from the feet of geckos. Another example of bioinspiration has come from the study of the optical properties of butterflies and moths, particularly in the way that they use nanostructures to create color, transparency, and hydrophobicity. Physicists have been quite successful in understanding the nanostructures that create these properties, but replicating them has been difficult and expensive. Here I will describe our approach to understanding how butterfly scales actually build such nanostructures, focusing on creating structural blue and green in Buckeye butterflies, and transparent wings in a variety of Neotropical butterflies. While our goal is to understand the basic biology behind such processes, we hope that they might also lead to easier ways to replicate them for other applications.

ANL All Hand’s Meeting
Lab wide safety refresh. Focus on the change in work environment and practices as APS begins the Upgrade Project.