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Decoding the shift-invariant data: applications for band-excitation scanning probe microscopy [article]

Yongtao Liu, Rama K. Vasudevan, Kyle Kelley, Dohyung Kim, Yogesh Sharma, Mahshid Ahmadi, Sergei V. Kalinin, Maxim Ziatdinov
2021 arXiv   pre-print
The shift VAE is extended towards the analysis of band-excitation piezoresponse force microscopy (BE-PFM) data, disentangling the resonance frequency shifts from the peak shape parameters in a model-free  ...  A shift-invariant variational autoencoder (shift-VAE) is developed as an unsupervised method for the analysis of spectral data in the presence of shifts along the parameter axis, disentangling the physically-relevant  ...  Following the invention of Atomic Force Microscopy (AFM) in 1986, 1 scanning probe microscopy (SPM) has emerged as an extremely powerful for probing and modifying nanoscale systems.  ... 
arXiv:2104.10207v1 fatcat:24zn5px43ffdbhh57tbwslwqkm

Describing condensed matter from atomically resolved imaging data: from structure to generative and causal models [article]

Sergei V. Kalinin, Ayana Ghosh, Rama Vasudevan, Maxim Ziatdinov
2021 arXiv   pre-print
The development of high-resolution imaging methods such as electron and scanning probe microscopy and atomic probe tomography have provided a wealth of information on structure and functionalities of solids  ...  At the same time, a wealth of local data allows fundamentally new approaches for the description of solids based on construction of statistical and physical generative models, akin to Ginzburg-Landau thermodynamic  ...  The recent development of the rotational-and shift-invariant variational autoencoders allows for further progress, assuming the shift invariance is sufficient to compensate for sampling.  ... 
arXiv:2109.07350v1 fatcat:jfj57u24izgltkj3a4emvmjmte

Optical nanoscopy

A. Diaspro, P. Bianchini
2020 La Rivista del nuovo cimento della Società italiana di fisica  
Moreover, the integration of optical nanoscopy with scanning probe microscopy and the charming possibility of using artificial intelligence approaches will be shortly outlined.  ...  This article deals with the developments of optical microscopy towards nanoscopy.  ...  Acknowledgements Open access funding provided by Istituto Italiano di Tecnologia within the CRUI-  ... 
doi:10.1007/s40766-020-00008-1 fatcat:zh6q4ion6bczfmhtwvc6j6gyry

Unsupervised Hyperspectral Stimulated Raman Microscopy Image Enhancement: Denoising and Segmentation via One-Shot Deep Learning [article]

Pedram Abdolghader, Andrew Ridsdale, Tassos Grammatikopoulos, Gavin Resch, Francois Legare, Albert Stolow, Adrian F. Pegoraro, Isaac Tamblyn
2021 arXiv   pre-print
Furthermore, by applying a k-means clustering algorithm to the processed data, we demonstrate automatic, unsupervised image segmentation, yielding, without prior knowledge of the sample, intuitive chemical  ...  Hyperspectral stimulated Raman scattering (SRS) microscopy is a label-free technique for biomedical and mineralogical imaging which can suffer from low signal to noise ratios.  ...  The authors declare that there are no conflicts of interest related to this article. Data Availability. All data used in this study is available at Ref. [48] .  ... 
arXiv:2104.08338v2 fatcat:adtokz4pwndxhksoqr54or2oee

The role of convolutional neural networks in scanning probe microscopy: a review

Ido Azuri, Irit Rosenhek-Goldian, Neta Regev-Rudzki, Georg Fantner, Sidney R Cohen
2021 Beilstein Journal of Nanotechnology  
Scanning probe microscopy measures multimodal surface properties, combining morphology with electronic, mechanical, and other characteristics.  ...  In this review, we focus on a subset of deep learning algorithms, that is, convolutional neural networks, and how it is transforming the acquisition and analysis of scanning probe data.  ...  We further are deeply indebted to the reviewers of this manuscript for providing useful and comprehensive feedback.  ... 
doi:10.3762/bjnano.12.66 pmid:34476169 pmcid:PMC8372315 fatcat:dwl2mqxfjnanve363my7qr4try

Computational Methods for Single-Cell Imaging and Omics Data Integration

Ebony Rose Watson, Atefeh Taherian Fard, Jessica Cara Mar
2022 Frontiers in Molecular Biosciences  
Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques  ...  This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further  ...  The applications of methods for sc-RNA data analysis have begun to evolve into a predictable workflow.  ... 
doi:10.3389/fmolb.2021.768106 pmid:35111809 pmcid:PMC8801747 fatcat:zrqpododa5gyxoti5fnx3llepq

Automated and Autonomous Experiment in Electron and Scanning Probe Microscopy [article]

Sergei V. Kalinin, Maxim A. Ziatdinov, Jacob Hinkle, Stephen Jesse, Ayana Ghosh, Kyle P. Kelley, Andrew R. Lupini, Bobby G. Sumpter, Rama K. Vasudevan
2021 arXiv   pre-print
Here, we aim to analyze the major pathways towards AE in imaging methods with sequential image formation mechanisms, focusing on scanning probe microscopy (SPM) and (scanning) transmission electron microscopy  ...  data analysis.  ...  ) in optical imaging and Band Excitation 127, 128 in SPM.  ... 
arXiv:2103.12165v1 fatcat:z3uh2jxrgfbf7d4kol6ed6bcra

Noise performance of frequency modulation Kelvin force microscopy

Heinrich Diesinger, Dominique Deresmes, Thierry Mélin
2014 Beilstein Journal of Nanotechnology  
Probe merit factors for both cases are then established, suggesting how to tackle noise performance by probe design. Typical merit factors of common probe types are compared.  ...  A design rule is proposed that allows choosing the AC modulation frequency for optimized sharing of the PLL bandwidth between Kelvin and topography loops.  ...  Acknowledgements This work was achieved with the financial support of the European Union, the French Government and the Regional Council, using the facilities of the EXCELSIOR Nanoscience Characterization  ... 
doi:10.3762/bjnano.5.1 pmid:24455457 pmcid:PMC3896264 fatcat:binavwewynh6ziyh4xoczkjxmm

Fast scanning high optical invariant two-photon microscopy for monitoring a large neural network activity with cellular resolution [article]

Keisuke Ota, Yasuhiro Oisi, Takayuki Suzuki, Muneki Ikeda, Yoshiki Ito, Tsubasa Ito, Kenta Kobayashi, Midori Kobayashi, Maya Odagawa, Chie Matsubara, Yoshinori Kuroiwa, Masaru Horikoshi (+9 others)
2020 bioRxiv   pre-print
The result is a practically aberration-free, fast scanning high optical invariant two-photon microscopy (FASHIO-2PM) that enables calcium imaging from a large network composed of ~16k neurons at 7.5 Hz  ...  Here, we overcome the tradeoffs by combining a resonant scanning system, a large objective with low magnification and high numerical aperture, and highly sensitive large-aperture photodetectors.  ...  high optical invariant 121 (0.6 for excitation and 1.2 for collection) two-photon microscopy (FASHIO-2PM) (see 122 Table S1 for acquisition modes).  ... 
doi:10.1101/2020.07.14.201699 fatcat:6bqfoubllrde3f4gjmnjpzeux4

An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)

Björn Harink, Huy Nguyen, Kurt Thorn, Polly Fordyce, Vadim E. Degtyar
2019 PLoS ONE  
Here, we present a novel open-source Python software package (the mrbles analysis package) that provides the necessary tools to: (1) find encoded beads in a bright-field microscopy image; (2) quantify  ...  Multiplexed bioassays, in which multiple analytes of interest are probed in parallel within a single small volume, have greatly accelerated the pace of biological discovery.  ...  While we present this package as a method for decoding MRBLEs, mrbles should be broadly applicable to decoding and quantifying binding to unencoded beads as well as beads embedded with any ratiometric  ... 
doi:10.1371/journal.pone.0203725 pmid:30901328 pmcid:PMC6430362 fatcat:qdgir666ajg4vdkk7c4tvrnfqm

Analysis strategies for high-resolution UHF-fMRI data

Jonathan R. Polimeni, Ville Renvall, Natalia Zaretskaya, Bruce Fischl
2018 NeuroImage  
Most UHF-fMRI studies utilize the dramatic increases in sensitivity and specificity to acquire high-resolution data reaching sub-millimeter scales, which enable new classes of experiments to probe the  ...  Functional MRI (fMRI) benefits from both increased sensitivity and specificity with increasing magnetic field strength, making it a key application for Ultra-High Field (UHF) MRI scanners.  ...  Programme for research, technological development and demonstration under grant agreement No. 605728; and by the German Excellence Initiative through the Centre for Integrative Neuroscience Tübingen (  ... 
doi:10.1016/j.neuroimage.2017.04.053 pmid:28461062 pmcid:PMC5664177 fatcat:dcrrvh4sgfcb5diw62bgbeng2a

P3C-6 Role of Ultrasonic Velocity Estimation Errors in Assessing Inflammatory Response and Vascular Risk

S. I. Simon, J. K. Tsou, M. F. Insana
2006 2006 IEEE Ultrasonics Symposium  
The feasibility of coded-pulse excitation implemented for ultrasonic shear rate imaging is examined for both in vitro phantom and in vivo imaging.  ...  We apply broadband coded excitation techniques with compression on the received signals to demonstrate an increase in eSNR while maintaining high image resolution.  ...  stationary and h d is shift invariant.  ... 
doi:10.1109/ultsym.2006.518 fatcat:sis5slw4czhyxespuntb2h6jvq

Computational Plenoptic Imaging [article]

Gordon Wetzstein, Ivo Ihrke, Douglas Lanman, Wolfgang Heidrich
2011 Eurographics State of the Art Reports  
The plenoptic function is a ray-based model for light that includes the color spectrum as well as spatial, temporal, and directional variation.  ...  convert photons into electrons; in the process, all visual information is irreversibly lost, except for a two-dimensional, spatially-varying subset - the common photograph.  ...  This project was in part supported by the GRAND NCE. Ivo Ihrke was supported by the DFG Cluster of Excellence "Multimodal Computing and Interaction".  ... 
doi:10.2312/eg2011/stars/025-048 fatcat:573egkiky5da3ozhozfpmrm254

Computational plenoptic imaging

Gordon Wetzstein, Ivo Ihrke, Douglas Lanman, Wolfgang Heidrich, Ramesh Raskar, Kurt Akeley
2012 ACM SIGGRAPH 2012 Posters on - SIGGRAPH '12  
The plenoptic function is a ray-based model for light that includes the color spectrum as well as spatial, temporal, and directional variation.  ...  convert photons into electrons; in the process, all visual information is irreversibly lost, except for a two-dimensional, spatially-varying subset -the common photograph.  ...  This project was in part supported by the GRAND NCE. Ivo Ihrke was supported by the DFG Cluster of Excellence "Multimodal Computing and Interaction".  ... 
doi:10.1145/2343483.2343494 fatcat:uqvwuaaeznej3oiq7gfxtbj3pu

Computational Plenoptic Imaging

Gordon Wetzstein, Ivo Ihrke, Douglas Lanman, Wolfgang Heidrich
2011 Computer graphics forum (Print)  
The plenoptic function is a ray-based model for light that includes the colour spectrum as well as spatial, temporal and directional variation.  ...  convert photons into electrons; in the process, all visual information is irreversibly lost, except for a two-dimensional, spatially varying subset-the common photograph.  ...  For each of the plenoptic dimensions we also discuss practical applications of the acquired data.  ... 
doi:10.1111/j.1467-8659.2011.02073.x fatcat:algvg77lkjevlov7stqcf7eh2q
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