HRTEMFringeAnalyzer a free python module for an automated analysis of fringe pattern in transmission electron micrographs

A python module (HRTEMFringeAnalyzer) is reported to evaluate the local crystallinity of samples from high‐resolution transmission electron microscopy images in a mostly automated fashion. The user only selects the size of a square analyser window and a step size which translates the window in the micrograph. Together they define the resolution of the results obtained. Regions where fringe patterns are visible are identified and their lattice spacing d and direction ϕ as well as the corresponding mean errors σ determined. 1/σd is proportional to the coherence length of the structure, whereas σφ is a measure of how well the direction of the fringes is defined. Maps of these four indicators are computed. The performance of the program is demonstrated on two very different samples: ill‐crystalline carbon deposits on a coked Ni/LFNO (reduced LaFe0.8Ni0.2O 3±δ ) catalyst and well‐crystallized nanoparticles of zinc doped ceria. In the latter case, the automatic segmentation of large aggregates into individual crystalline domains is achieved by ϕ maps.

[1]  Bernard Delmon,et al.  Preparation of Highly Dispersed Mixed Oxides and Oxide Solid Solutions by Pyrolysis of Amorphous Organic Precursors , 1970 .

[2]  Hejun Li,et al.  Analysis Techniques of Lattice Fringe Images for Quantified Evaluation of Pyrocarbon by Chemical Vapor Infiltration , 2014, Microscopy and Microanalysis.

[3]  Michael Unser,et al.  Transforms and Operators for Directional Bioimage Analysis: A Survey. , 2016, Advances in anatomy, embryology, and cell biology.

[4]  J Sijbers,et al.  StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images. , 2016, Ultramicroscopy.

[5]  Eric Jones,et al.  SciPy: Open Source Scientific Tools for Python , 2001 .

[6]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[7]  M. Hytch,et al.  Analysis of Variations in Structure from High Resolution Electron Microscope Images by Combining Real Space and Fourier Space Information , 1997 .

[8]  Z Q Liu,et al.  Scale space approach to directional analysis of images. , 1991, Applied optics.

[9]  Ron Jenkins,et al.  Introduction to X-ray Powder Diffractometry: Jenkins/Introduction , 1996 .

[10]  Xiaoyan Song,et al.  Characterization of grain structure in nanocrystalline gadolinium by high-resolution transmission electron microscopy , 2009 .

[11]  Thomas Tybell,et al.  Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting , 2017, Advanced Structural and Chemical Imaging.

[12]  D. Ferri,et al.  Structural Reversibility and Nickel Particle stability in Lanthanum Iron Nickel Perovskite-Type Catalysts. , 2017, ChemSusChem.

[13]  Owen Robert Mitchell,et al.  Precision Edge Contrast and Orientation Estimation , 1988, IEEE Trans. Pattern Anal. Mach. Intell..

[14]  Maxim Ziatdinov,et al.  Phases and Interfaces from Real Space Atomically Resolved Data: Physics-Based Deep Data Image Analysis. , 2016, Nano letters.

[15]  A. Wokaun,et al.  Structural and chemical changes of Zn-doped CeO2 nanocrystals upon annealing at ultra-high temperatures , 2015 .

[16]  Pierre Baylou,et al.  A new adaptive framework for unbiased orientation estimation in textured images , 2005, Pattern Recognit..

[17]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[18]  Ron Jenkins,et al.  Introduction to X-ray powder diffractometry , 1996 .

[19]  Gaël Varoquaux,et al.  The NumPy Array: A Structure for Efficient Numerical Computation , 2011, Computing in Science & Engineering.

[20]  A. Wokaun,et al.  Zn-modified ceria as a redox material for thermochemical H2O and CO2 splitting: effect of a secondary ZnO phase on its thermochemical activity , 2016 .

[21]  GEOMETRIC PHASE ANALYSIS OF HIGH RESOLUTION ELECTRON MICROSCOPE IMAGES , 2003 .

[22]  A. Wokaun,et al.  Correlation between the structural characteristics, oxygen storage capacities and catalytic activities of dual-phase Zn-modified ceria nanocrystals , 2015 .