Useful Resources

This page provides a non-exhaustive list of useful resources.

• Multi-purpose image processing in ImageJ/Fiji:

  • Creating colour composites/false colour images
  • Handling 3D or slice & view data
  • Segmentation of images (i.e. separating out different features, also useful for 3D reconstruction)
  • Particle analysis, e.g. size distributions
  • Image stitching and alignment for montages
  • Import image sequences as stacks and synchronise those image stacks (e.g. if you have images of the same thing from different detectors)

• Electron diffraction pattern analysis:

  • CrysTBox: numerous tools for indexing patterns, especially useful for complex phases where you want to use a CIF to figure out the zone axis for example. Has loads of other capabilities as well.
  • Odpin: simple browser-based tool for indexing SAD patterns
  • Get dSpace: ImageJ plugin for automatically measuring the d-spacings of reflections in SAD patterns.
  • Radial Profile Plot: ImageJ plugin for calculating the radial profile for polycrystalline (ring) diffraction patterns
  • Recipro: program for various crystallographic calculations/visualisations including unit cells & single crystal diffraction patterns, can also index SAD.

• EBSD data processing:

  • ATEX: nice user-friendly interface, plenty of tools
  • MTEX: Matlab-based command line toolbox
  • Kikuchipy: Python API with extensive tools for re-indexing, can be used in conjunction with HyperSpy to handle EDX data.

• Spectroscopy (EDX, EELS) data processing:

  • HyperSpy: An incredibly extensive Python API, forms the basis of numerous off-shoots. Can import most of the commonly used data types.
  • DTSA-II: software from NIST for quantification of EDX spectra.

• (S)TEM data processing:

  • Atomap: Python library for analysing atomic resolution STEM images via Gaussian fitting to the atomic columns. Allows for strain analysis, etc.
  • TEMMETA: another Python library allowing you do most of the commonly used stuff such as Fourier filtering, geometric phase analysis (GPA) for strain analysis, etc.
  • Strain++: program for performing GPA on high resolution (S)TEM images for strain mapping.
  • Recipro: program for various crystallographic calculations/visualisations including unit cells & single crystal diffraction patterns.

• Databases:

  • ICSD: inorganic crystal structure database
  • Crystallography open database (free)
  • American Mineralogist Crystal Structure Database: good for geological stuff
  • NIST X-ray transition energies search form: useful for EDX
  • EELS Atlas: online version of Gatan’s thing, gives lots of info about EELS edge energies, etc.
  • EELS DB: database of example EEL spectra
  • Ptable: interactive periodic table with oxidation states, properties, etc.
  • XPS Periodic Table: basically an XPS version of the EELS Atlas
  • NIST XPS Database
  • Raman Open Database
  • RRUFF: database of Raman spectra for minerals

• Selective colourisation in GIMP

• Textbooks/reference:

  • Transmission Electron Microscopy: A Textbook for Materials Science: the definitive textbook for TEM
  • Advanced Transmission Electron Microscopy: another good TEM reference
  • Rodenburg.org: online TEM reference
  • Globalsino.com: another handy TEM reference
  • Quantify Extracted Signal: info about quantifying EEL spectra
  • Scanning Electron Microscopy and X-Ray Microanalysis: comprehensive textbook about SEM/EDX