pycotem: An open source toolbox for online crystal defect characterization from TEM imaging and diffraction

Abstract

We present a series of tools working together that facilitate the determination of dislocation Burgers vectors and slip planes, interface plane normals and misorientation between two crystals from a series of Transmission Electron Microscopy (TEM) micrographs and diffraction patterns. To that purpose, we developed graphical user interface programs that allow crystal orientation determination from spot diffraction patterns taken at various tilt angles or from Kikuchi patterns crystal representation from stereographic projection plots and determination of geometrical features from series of conventional images taken at different tilt angles. We present working examples that allow a faster and easier way to analyse data that can especially be retrieved during in situ straining experiments where dislocations and grain boundaries need to be characterized. More generally, these tools target material scientists interested in daily microstructural characterization in TEM.

High temperature plasticity at twin boundary in Al: An in-situ TEM perspective

“…Video sequences were recorded at 25 fps using a MEGAVIEW III camera and a mp4 encoding capture device. Crystal orientation, misorientation, planes/directions determination was derived from electron diffraction and conventional Bright Field/Dark Field (BF/DF) imaging, using pycotem [42]. When several imaging conditions are available, disconnection Burgers vectors can be determined by analyzing their contrast features [35].…”

Study of the epitaxy between ɛ-Fe2O3, hematite and spinel in brown-glazed Chinese ceramics using electron diffraction mapping techniques

“…Orientation data processing. The relationships between the different phases were deduced from TKD and ACOM-PED maps by using the Misorientation software from the Pycotem software suite (Mompiou & Xie, 2021), which enables the drawing of superposed pole figures of crystals from two different phases. The possibility of epitaxy between different phases suggested by Misorientation was studied by displaying the structures given by the CIFs ICSD-51122 for "-Fe 2 O 3 (Tronc et al, 1998), ICDD-01-071-5088 for hematite, COD-1540775 for spinel (Zorina & Kvitka, 1969) and ICDD-00-046-1212 for corundum with the VESTA 3.5.7 software (Momma & Izumi, 2011) and calculating the O-O distances from these.…”

Data-Mining of In-Situ TEM Experiments: On the Dynamics of Dislocations in CoCrFeMnNi Alloys

“…A detailed discussion and python implementation details are given in [26]. Our TEM data were processed with the open-source software pycotem [27] where right-handed coordinate systems and active rotations are used. Furthermore, the software follows the Bunge convention with intrinsic rotations.…”