Method development

Software development

Method-developmentDr. Probe Light user interface showing a partially coherent probe on the right.
Copyright: FZ Jülich, ER-C

Scientists in the ER-C develop software for electron microscopy and spectroscopy.

Available software includes:

  • CMP (chemical mapping package)
  • DCISim (diffraction contrast image simulation notebook)
  • Dr. Probe light (STEM probe and Ronchigram simulation software)
  • Dr. Probe (HR(S)TEM image simulation package)
  • Gempa (general electron micrograph processing & analysis software
  • Holography package for HyperSpy (reconstruction and processing of off-axis electron holograms)
  • ImageConverter (multi-platform image conversion tool)
  • iMtools (general purpose multi platform image processing tools)
  • P_SpaceChargeLight (tunnel current simulation software package)
  • PantaRhei (TEM optical stability benchmark)
  • tomato (multi-platform tomography suite)
  • Spring (processing suite for high resolution structure determination of EM samples with helical geometry)


  • LocScale (density scaling/sharpening procedure to enhance interpretability of cryo-EM maps)


  •  FDRthresholding (density interpretation tool to analyze cryo-EM maps using „false discovery rate“ background noise estimation)


  • FDR-FSC (Online mask-less resolution estimation of cryo-EM maps)


  • SPOC (Statistical Processing of cryo-EM maps)


Custom-made TEM hardware components

Method-developmentTest chamber for instrumentation development
Copyright: FZ Jülich, ER-C

New instrumentation that is not available commercially is developed in collaboration with academic and corporate partners. Our technical staff advise and support scientists to develop innovative solutions based on feasibility studies.

A wide spectrum of new instruments is developed and constructed on site, including:

  • TEM sample holders and cartridges
  • TEM aperture holders with electrical contacts
  • FIB flip stages for needles and chips
  • SEM sample stages with electrical contacts
  • A copy of a TEM octagon for testing custom-made sample holders and apertures
  • Mounting, assembly and storage systems for TEM sample and aperture holders
  • A pumping station for TEM sample holders