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These programs calculate high resolution conventional and scanning transmission electron microscope (CTEM, STEM) images of thin specimens from first principles using the multislice method for electrons in the energy range of approximately 60 keV to 1000 keV. The fundamental theory and usage are described in "Advanced Computing in Electron Microscopy" (Springer 2020) and Acta Cryst. A72 (2016) p. 1 by Earl J. Kirkland. Please refer to these for the theory of calculation and how to use these programs.
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The Artificial SEM Image Generator (ARTIMAGEN) is a library that generates artificial scanning electron microscope (SEM) and helium-ion microscope images of various samples, including gold-on-carbon resolution sample, or some semiconductor features.
instrument control, data acquisition display and analysis
...Interfaces accessible via commands and scripts: file i/o modelled on stdio and stdlib; usb control and bulk transfers; socket operations; webcam; graphics via framebuffer.
Applications (not all available yet for download) include: cell poker (like an atomic force microscope); tissue mechanical tester; fluorescence photobleaching; alternating laser excitation fluorescence; fluorescence intensity distribution analysis; iverilog simulation analysis.
ACCORD is a C library for composition of scanning electron or helium-ion microscope images with correction of drift. It produces significantly more accurate images than the traditional imaging techniques and also provides drift trajectories.
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...I'd like to clean it up and improve the back end design when time permits. See the wiki for known issues and more information.
A computer vision program for analysis of magnetic data collected by a scanning probe microscope. Originated in summer 2007 as a collection of C compiled for Matlab (MEX) files and was eventually ported to a standalone C++ application with a GUI created in Qt.
This program takes atomic and magnetic force microscope (AFM/MFM) image pairs as input and uses threshold segmentation to identify magnetic nanodots by intensity in the AFM image. ...
A software tool enabling the user to browse through an image stack created by a confocal microscope. Points can be plotted through the stack, producing a digital 3D representation, which can be viewed in 3D and compared with other plots.
The virtual lab is a NASA-funded project to provide simulated instrumentation. ITG has developed a Virtual Microscope (Virtual SEM and LM) for viewing high-resolution, multi-dimensional image datasets. More info and data: http://virtual.itg.uiuc.edu
Micro-manager is software that controls your microscope. It orchestrates digital cameras, shutters, filter wheels, stages and other motorized components to let scientists/engineers acquire images from the microworld the way they want.