Computers
There are five workstations available for general use with varying amounts of RAM in the computer room on the second floor. All of them are networked to the NCEM data storage and in most cases networked to the support PCs of the microscopes. There is signage in the computer room regarding the details of each workstation. Two of the workstations are available by reservation only, allowing uninterrupted remote use and scheduled analysis time.
Commercial and Free Software
Digital Micrograph A general TEM image processing software provided by Gatan Inc. Several plugins are available such as EELS and 4D-STEM.
TIA Analysis software for STEM and EELS data provided by FEI. Opens EMI/SER files.
Velox EDS, STEM, TEM analysis by ThermoFisher
Esprit EDS analysis by Bruker
ImageJ/FIJI General open source image processing
Single Crystal/Crystal Maker/Crystal Diffract Crystal viewing/manipulation and diffraction simulation
Zoom speakers and microphones are available for zoom meetings
IMOD Electron tomography alignment and reconstruction software
Tomviz Free and open source electron tomography alignment, reconstruction, and volume visualization software
Custom Analysis Code
- py4DSTEM
- Open source analysis code for analyzing 4D-STEM datasets developed by Colin Ophus and his group.
- Download code and tutorials here: https://github.com/py4dstem/py4DSTEM
- Prismatic
- A CUDA/C++/Python software package for fast image simulation in scanning transmission electron microscopy (STEM) and high-resolution transmission electron microscopy (HRTEM).
- Includes parallel, data-streaming implementations of both the plane-wave reciprocal-space interpolated scattering matrix (PRISM) and multislice algorithms using multicore CPUs and CUDA-enabled GPU(s), in some cases achieving accelerations as high as 1000x or more relative to traditional methods.
- Prismatic is fast, free, open-sourced, and contains a graphical user interface.
- MATLAB Multislice Simulations
- Custom software routines for simulating images and diffraction patterns in TEM and STEM using a large number of scripts developed by Colin.
- Methods are given in Earl Kirkland’s textbook “Advanced Computing in Electron Microscopy,” second edition.
- Can be used to simulate virtually any scale of problem and vary any structural, chemical or optical parameter.
- MATLAB Focal Series Reconstruction
- Code for reconstructing HRTEM exit wave phase with high accuracy, written by Colin.
- EMD Format and EMDviewer
- An open-source data format for microscopy data of any type, having an arbitrary number of data dimensions.
- Useful for visualization of extremely large experimental and simulated datasets.
- Can also be used to render movie frame images for use with FFMPEG.
- Can be downloaded for free here.
