Pycro-Manager: open-source software for customized and reproducible microscope control

November 19, 2021|

Innovative microscopy techniques are often impeded by a lack of control software that is capable of meeting demands for speed and performance, integrating new and diverse types of hardware, providing the flexibility to adapt in real time to the data being captured, and providing user-friendly programming interfaces. As a result, researchers often end up developing custom software that works only with specific instruments, using closed-source and/or proprietary programming languages. Pycro-Manager is a package that meets these challenges by enabling python control of Micro-Manager (an open-source microscopy control software) as well as the simple development of customized experiments that involve microscope hardware control integrated with real-time image processing. It is compatible with hundreds of microscope components and full microscopes and provides open source APIs for the integration of new hardware. More information can be found at:

H. PinkardN. StuurmanI. E. IvanovN. M. AnthonyW. OuyangB. LiB. YangM. A. TsuchidaB. ChhunG. ZhangR. MeiM. AndersonD. P. ShepherdI. Hunt-IsaakR. L. DunnW. JahrS. KatoL. A. RoyerJ. R. ThiagarajahK. W. EliceiriE. LundbergS. B. MehtaL. Waller, "Pycro-Manager: open-source software for customized and reproducible microscope control," Nature Methods18226-228(2021). DOI: 10.1038/s41592-021-01087-6

2D vibrational exciton nano-imaging of domain formation in self-assembled monolayer

November 16, 2021|

Understanding the chemical and physical properties of surfaces at the molecular level is highly relevant in the fields of medicine, semiconductors, batteries, etc. where precise atomic level control of determines materials and device performance. In particular, molecular order and domains affect many of the desired functional properties with carrier transport, wettability, and chemical reactivity often controlled by intermolecular coupling. However, both imaging of molecular surfaces and spectroscopy of molecular coupling has long been challenged by limited chemically specific contrast, spatial resolution, sensitivity, and precision. In this work, a team of  STROBE researchers demonstrate vibrational excitons as a molecular ruler of intermolecular coupling and quantum sensor for wave function delocalization to image nanodomain formation in self-assembled monolayers. In novel precision spatio-spectral infrared scattering scanning near-field optical microscopy combined with theoretical modelling few nanometer domain sizes and their distribution across micron scale fields of view could be resolved. This approach of vibrational exciton nanoimaging is generally applicable to study structural phases and domains in a wide range of molecular interfaces and the method can be used for engineering better molecular interfaces, with controlled properties for molecular electronic, photonic, or biomedical applications.

T. P. GrayJ. NishidaS. C. JohnsonM. B. Raschke, "2D Vibrational Exciton Nanoimaging of Domain Formation in Self-Assembled Monolayers," Nano Letters215754-5759(2021). DOI: 10.1021/acs.nanolett.1c01515

Cool it: Nano-scale discovery could help prevent overheating in electronics

November 8, 2021|

A team of physicists and engineers at CU Boulder have solved the mystery behind a perplexing phenomenon in the nano realm: why some ultra-small heat sources cool down faster if you pack them closer together. The research began with an unexplained observation: a team led by Margaret Murnane and Henry Kapteyn at JILA were experimenting with metallic nanolines on a silicon substrate that when heated with a laser, something strange occurred. Nanoscale heat sources do not usually dissipate heat efficiently. But if you pack them close together, they cool down much more quickly.

Now, the researchers know why it happens. The team joined forces with a group of theorists led by Mahmoud Hussein in Aerospace Engineering Sciences to use computer-based simulations to track the passage of heat from their nano-sized bars. The simulations were so detailed that they could follow the behavior of each and every atom in the model—millions of them in all. They discovered that when they placed the heat sources close together, the vibrations of energy (called phonons) they produced bounced off each other more efficiently when other heat sources were nearby, scattering heat away and cooling the bars down.

The group’s results highlight a major challenge in designing the next generation of tiny devices, such as microprocessors or quantum computer chips. When you shrink down to very small scales, heat does not always behave the way you think it should.

H. HonarvarJ. L. KnoblochT. D. FrazerB. AbadB. McBennettM. I. HusseinH. C. KapteynM. M. MurnaneJ. N. Hernandez-Charpak, "Directional thermal channeling: A phenomenon triggered by tight packing of heat sources," Proceedings of the National Academy of Sciences118e2109056118(2021). DOI: 10.1073/pnas.2109056118

Three-dimensional atomic packing in amorphous solids with liquid-like structure

October 18, 2021|

Liquids and solids are two fundamental states of matter. Although the structure of crystalline solids has long been solved by crystallography, our understanding of the 3D atomic structure of liquids and amorphous materials remained speculative due to the lack of direct experimental determination. Now, a collaborative team from UCLA, Lawrence Berkeley National Lab and Brown University has advanced atomic electron tomography to determine for the first time the 3D atomic positions in monatomic amorphous materials, including a Ta thin film and two Pd nanoparticles. Despite different chemical composition and synthesis methods, they observed that pentagonal bipyramids are the most abundant atomic motifs in these amorphous materials. Contrary to traditional understanding, most pentagonal bipyramids do not assemble icosahedra, but are closely connected to form networks extending to medium-range scales. Molecular dynamics simulations further revealed that pentagonal bipyramid networks are prevalent in monatomic metallic liquids, which rapidly grow in size and form more icosahedra during the quench from the liquid to the glass state. These results expand our fundamental understanding of the atomic structure of amorphous solids and will encourage future studies on amorphous-crystalline phase and glass transitions in non-crystalline materials with three-dimensional atomic resolution.

Y. Yuan, D.S. Kim, J. Zhou, D.J. Chang, F. Zhu, Y. Nagaoka, Y. Yang, M. Pham, S. J. Osher, O. Chen, P. Ercius, A. K. Schmid and J. Miao, “Three-dimensional atomic packing in amorphous solids with liquid-like structure”, Nature Materials, (2021). DOI: 10.1038/s41563-021-01114-z

Investigating the potential for entangled two-photon excited fluorescence imaging

May 21, 2021|

Setting bounds on the absorption cross-sections of molecular systems. There has been a long-running controversy regarding the “quantum advantage” for multiphoton excitation of molecules with entangled photons and if quantum multiphoton imaging can be realized. Although theoretical proposals have been advanced for decades, no experimental work (with the exception of a publication by Jeff Kimble’s group in the 1990s) appeared in the literature until 2006 when reports from a small number of groups began to emerge of a large quantum enhancement (e.g. up to 10 orders of magnitude) of the two photon excitation rate using entangled pairs compared to classical light. Last year, a paper describing a microscope based on the “entangled two-photon absorption” (E2PA) effect was published in Journal of the American Chemical Society. On the other hand, it has emerged from discussions at scientific meetings that many researchers have failed to replicate the results in these numerous publications, or to find any other evidence for this enhancement. As a result, there is considerable skepticism of the publications making these remarkable claims. Unfortunately, these negative results haven’t been published and therefore a rigorous basis for resolving the controversy hasn’t yet been established. Finally, new experiments at JILA have finally set upper-bounds for the E2PA cross-sections in molecular fluorophores, including those investigated in previous reports. We performed both classical and quantum light excitation in the same optical transmission and fluorescence-based systems with rigorously characterized states of light and measurement sensitivities. We find that E2PA cross-sections are at least four to five orders of magnitude smaller than previously reported. Our results imply that the signals and images reported in previous publications are artifacts. Although we don’t expect this contribution to be the last word on the subject, this work introduces a new level of experimental rigor that will lead towards new designs for quantum microscopes and sensors.

M. Parzuchowski, A. Mikhaylov, M. D. Mazurek, R. N. Wilson, D. J. Lum, T. Gerrits, C. H. Camp, M. J. Stevens, R. Jimenez, “Setting Bounds on Entangled Two-Photon Absorption Cross Sections in Common Fluorophores,” Physical Review Applied, 15, 044012 , (2021).

Nondestructive, high-resolution, chemically specific 3D nanostructure characterization using phase-sensitive EUV imaging reflectometry

May 20, 2021|

Next-generation nano and quantum devices have increasingly complex 3D structure. As the dimensions of these devices shrink to the nanoscale, their performance is often governed by interface quality or precise chemical or dopant composition. A STROBE team from CU Boulder, UCLA, UC Berkeley, as well as laser and nanoelectronics industry partners, worked together for 4 years to design, construct and commission the first phase-sensitive extreme ultraviolet imaging reflectometer. It combines the excellent phase stability of tabletop coherent extreme UV (EUV) light sources, the unique chemical- and phase-sensitivity of coherent EUV imaging, and state-of-the-art algorithms. This tabletop microscope can non-destructively probe surface topography, layer thicknesses, and interface quality, as well as dopant concentrations and profiles. High-fidelity imaging was achieved by implementing phase sensitive imaging at different angles, by using advanced methods to mitigate noise and artifacts in the reconstructed image, and by using a high-brightness, EUV source with excellent intensity and wavefront stability. These measurements were validated through multiscale electron and atomic force microscopy imaging to show that this approach has unique advantages compared with others. Critical to this project were new photon and electron-based imaging methods, advanced algorithms, unique samples, as well STROBE advances in tabletop coherent imaging in transmission and reflection mode. Several STROBE trainees received awards for this effort.

Tanksalvala, C. L. Porter, Y. Esashi, B. Wang, N. W. Jenkins, Z. Zhang, G. P. Miley, J. L. Knobloch, B. McBennett, N. Horiguchi, S. Yazdi, J. Zhou, M. N. Jacobs, C. S. Bevis, R. M. Karl, P. Johnsen, D. Ren, L. Waller, D. E. Adams, S. L. Cousin, C. Liao, J. Miao, M. Gerrity, H. C. Kapteyn, M. M. Murnane, “Nondestructive, high-resolution, chemically specific 3D nanostructure characterization using phase-sensitive EUV imaging reflectometry,” Science Advances, 7, eabd9667, (2021).

New phase retrieval methods enabled by the world’s fastest electron detector

May 19, 2021|

The need for rapid and accurate image analysis is increasing in electron microscopy studies of nanomaterials. With newly developed fast, high-efficiency electron detectors and automated imaging protocols, incorporating electron microscopy into high throughput materials design efforts is becoming possible. These new capabilities strongly motivate automated methods to extract relevant structural features, such as nanoparticle size, shape, and defect content, from high resolution transmission electron microscopy (HRTEM) data to link these features to bulk properties and study the influence of heterogeneity on bulk behavior. In general, protocols that surpass the accuracy of traditional image analysis and do not require time-consuming manual analysis are needed. Recent advances in image interpretation using deep learning using machine learning make it a promising route toward automatic interpretation of HRTEM micrographs.

In this STROBE collaboration, we demonstrate a pipeline to detect and classify regions of interest in HRTEM micrographs. Our pipeline uses a convolutional neural net (CNN) to identify crystalline regions (nanoparticles) from an amorphous background in the images, and then feeds individual regions of interest into a random forest classifier to detect whether or not they contain a crystallographic defect. Our CNN has a lightweight U-Net architecture and accurately segments a diverse population of nanoparticles with only a small number of training images. After segmentation, individual nanoparticle regions can be isolated and fed directly into existing python tools to extract size and shape statistics. To detect the presence of defects in nanoparticle regions, we implement a random forest classifier. We demonstrated the random forest classifier’s ability to detect stacking faults in the CdSe subset of identified nanoparticles. Both the CNN and classifier demonstrate state of the art performance at their respective tasks. While this work focuses on HRTEM images of nanoparticles supported on a carbon substrate, in principle the tool can be used to detect any regions of crystallinity in HRTEM data.

K. Groschner, C. Choi, M. C. Scott, “Machine Learning Pipeline for Segmentation and Defect Identification from High-Resolution Transmission Electron Microscopy Data,” Microscopy and Microanalysis, 1-8, (2021).

Compressive and adaptive nano imaging for enhanced speed and content

May 18, 2021|

Scattering scanning near-field optical microscopy (s-SNOM) provides for spectroscopic imaging from molecular to quantum materials with few nanometer deep sub-diffraction limited spatial resolution. However, conventional acquisition methods are often too slow to fully capture a large field of view spatio-spectral dataset. Through this collaboration, STROBE researchers, at CU Boulder and the ALS –Berkeley, demonstrated how the data acquisition time and sampling rate can be significantly reduced while maintaining or even enhancing the physical or chemical image information content. The novel data acquisition and mathematical concepts implemented are based on advanced data compressed sampling, matrix completion, and adaptive random sampling. This research is of particular interest in synchrotron based nano-imaging facilities. This work paves the way to true spatio-spectral chemical and materials nano-spectroscopy with a reduction of sampling rate by up to 30 times.

Labouesse, S. C. Johnson, H. A. Bechtel, M. B. Raschke, R. Piestun, “Smart Scattering Scanning Near-Field Optical Microscopy,” ACS Photonics, 7, 3346-3352, (2020).

Atomic structures determined from digitally defined nanocrystalline regions

May 17, 2021|

Three-dimensional (3D) structures of molecules determined from nanoscale regions of crystalline arrays could potentially illuminate the subtle differences that engender crystal defects or the multiple states accessible to subpopulations of molecules within an ensemble. A step toward this goal involves the extraction of meaningful diffraction data from 3D regions on the nanoscale. This is achieved using a near-parallel electron beam designed to illuminate sub-10nm regions of a sample. Scanning such a beam across a sample allows for digital logic to be applied to the measured data, facilitating the expostfacto assortment of information and reduction from desired 3D subvolumes.

A STROBE team from UCLA, UC Berkeley and LBNL collaborated to determine the first molecular structures determined by 4DSTEM. The structures were determined from a digitally defined subregion of a nanocrystal. After collecting TB of data, the team obtained reconstructions that revealed the atomic structure of a peptide, and showed that radiation damage imparted on the sample during data collection was not prohibitive for structure determination. Compared to other approaches, the approach allows for a much greater degree of control and obviates the need for spatial separation of samples. New methods, algorithms, enhanced microscopes and advanced sample preparation techniques developed by the STROBE collaboration were key to enabling the success of this project.

Gallagher-Jones, K. C. Bustillo, C. Ophus, L. S. Richards, J. Ciston, S. Lee, A. M. Minor, J. A. Rodriguez, “Atomic structures determined from digitally defined nanocrystalline regions,” IUCrJ, 7, (2020).

STROBE solved a century-old scientific problem: Determining the 3D atomic structure of amorphous solids

April 13, 2021|

Amorphous solids such as glass, plastics and rubber are ubiquitous in our daily life and have broad applications ranging from telecommunications to electronics and solar cells. However, due to the lack of any crystal-like long-range order, the traditional X-ray crystallographic methods for extracting the three-dimensional (3D) atomic arrangement of amorphous solids simply do not work. STROBE advanced atomic electron tomography to determine the 3D atomic positions and chemical species of an amorphous solid for the first time – with a stunning precision of 21 picometer. We found that instead of long-range order characteristic of crystals such as diamond, this amorphous metallic glass had regions of short- and medium-range order. Moreover, although the 3D atomic packing is disordered, some regions connect with each other to form crystal-like networks, which exhibit translational but no orientational order. Looking forward, we anticipate this approach will open the door to determining the 3D atomic coordinates of a wide range of amorphous solids, whose impact on non-crystalline solids may be comparable to the first 3D crystal structure solved by x-ray crystallography over a century ago.

Y. Yang, J. Zhou, F. Zhu, Y. Yuan, D. Chang, D. S. Kim, M. Pham, A. Rana, X. Tian, Y. Yao, S. Osher, A. K. Schmid, L. Hu, P. Ercius and J. Miao, “Determining the three-dimensional atomic structure of an amorphous solid”, Nature 592, 60–64 (2021).
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