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We got our EDAX system fi xed. At the end, we needed to replace the data processing board. Fortunately, we had one available in out lab from another EDAX system. T anks for the suggestions anyway Erico Freitas f reitas.erico@gmail.com Sun Dec 10


Image Anaysis: pycroscopy


We would like to bring to your attention the GitHub repository for the community-wide development of codes for image analytics (cleaning, feature extraction, analysis of atomic positions), hyperspectral unmixing of high-dimensional data (STEM-EELS, ptychography, SPM spectroscopies), and supporting universal fi le format. T e codes are realized via Jupyter notebooks that are straight- forward to use. T e site is:


https:pycroscopy.github.iopycroscopyabout.html . Additional description is provided below. Join the open-code movement! Pycroscopy is a free and community-driven python http:www.


python.org package for scientifi c analysis of imaging modalities such as scanning transmission electron microscopy, scanning probe microscopy, scanning tunneling spectroscopy, and X-ray diff raction microscopy.


Pycroscopy uses a data-centric model wherein the raw data collected from the microscope, results from analysis and processing routines are all written to standardized hierarchical data format (HDF5) fi les for traceability, reproducibility, and provenance. Pycroscopy uses an instrument-independent universal data format that facilitates the generalized representation of data from any instrument T e instrument-independent data format facilitates the development of a single and generalized version of analysis code to be reused for data from a variety of sources. T e universal data format and generalized codebase enables Pycroscopy to serve as the hub for community-driven imaging and microscopy research. Motivation: 1. Growing data sizes • Cannot use desktop computers for analysis • Need: High performance computing, storage resources and compatible, scalable fi le structures


2. Increasing data complexity • Sophisticated imaging and spectroscopy modes resulting in 5,6,7…dimensional data


• Need: Robust soſt ware and generalized data formatting 3. Multiple fi le formats • Diff erent formats from each instrument. Proprietary in most cases


• Incompatible for correlation • Need: Open, instrument independent data format 4. Disjoint communities • Similar analysis routines were written by each community (SPM, STEM, TOF SIMs, XRD…) independently!


• Need: Centralized repository, instrument agnostic analysis routines that bring communities together


5. Expensive analysis soſt ware • Soſt ware supplied with instruments oſt en insuffi cient incapable of custom analysis routines


• Commercial soſt ware (e.g., Matlab, Origin) are oſt en prohibitively expensive.


Need: Free, powerful, open source, user-friendly soſt ware 68 www.microscopy-today.com • 2018 March


Available tools in pycroscopy: Analysis: • Finding and refi ning atomic positions in atomically resolved images


• Reconstruction of current in ultra-fast current-voltage spectroscopy via Bayesian inference


• Fitting peaks to models in hyperspectral data o Fitting piezoresponse hysteresis loops to models Data processing:


• Statistical de-noising of images • Utilities to simplify clustering and decomposition of data • Feature extraction from images • Image transformations • FFT signal fi ltering File and data handling: • Utilities for advanced and fi le-safe writing • Ability to read, write, manipulate multi-dimensional hyperspectral datasets (1D – 8D and beyond) Translating from proprietary data formats:


• Band excitation imaging and spectroscopy • Time resolved Kelvin Probe force microscopy • I-V + First Order Reversal Curve spectroscopy General mode imaging and spectroscopy


• Asylum Research imaging and spectroscopy • Nanonis imaging and spectroscopy • Nion Co. scanning transmission electron microscopy imaging


• Omicron scanning tunneling spectroscopy • FEI Titan ptychography scanning transmission electron microscopy imaging


• Standard images – PNG, TIFF, etc. Visualization: • Tools for interactive visualization of complex multi- dimensional datasets


• Utilities for generating publication-ready plots Journal papers published using pycroscopy:


• “Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography,” https:www.nature .comarti- clessrep26348, Jesse et al., Scientifi c Reports (2015)


• “Rapid mapping of polarization switching through complete information acquisition,” http:www.nature. comarticlesncomms13290 , Somnath et al., Nature Communications (2016)


• “Improving superconductivity in BaFe2As2-based crystals by cobalt clustering and electronic uniformity,” http:www.nature.comarticless41598-017-00984-1 , Li et al., Scientifi c Reports (2017)


• “Direct Imaging of the Relaxation of Individual Ferroelectric Interfaces in a Tensile-Strained Film,” http:// onlinelibrary.wiley.comdoi10.1002aelm.201600508 full , Li et al.; Advanced Electronic Materials (2017)


• “Ultrafast Current Imaging via Bayesian Inference,” Somnath et al., accepted at Nature Communications (2017)


• “Decoding apparent ferroelectricity in perovskite nanofi - bers,” Ganeshkumar et al., accepted at ACS Applied Materials & Interfaces (2017)


• “Feature extraction via similarity search: application to atom fi nding and de-noising in electron and scanning probe microscopy imaging,” Somnath et al.; under review at Advanced Structural and Chemical Imaging (2017)


Sergei Kalinin sergei2@ornl.gov T u Dec 21


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