Method development

Software development

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

Available software includes:

• CMP (Chemical mapping package)
  More@www.er-c.org
• DCISim (diffraction contrast image simulation notebook)
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• Dr. Probe light (STEM probe and Ronchigram simulation software)
  More@www.er-c.org
• Dr. Probe (HR(S)TEM image simulation package)
  More@www.er-c.org
• Gempa (general electron micrograph processing & analysis software)
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• Holography package for HyperSpy (reconstruction and processing of off-axis electron holograms)
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• ImageConverter (multi-platform image conversion tool)
  More@www.er-c.org
• iMtools (general purpose multi platform image processing tools)
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• P_SpaceChargeLight (Tunnelstrom Simulation Softwarepaket)
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• PantaRhei (TEM optical stability benchmark)
• Tomato (multi-platform tomography suite)
  More@www.er-c.org
• Spring (single-particle based helical reconstruction software suite) More
• LocScale (Local density scaling/sharpening of cryo-EM maps) More
• FDRthresholding (Statistical density thresholding of cryo-EM maps using "false discovery rate" control)More
• FDR-FSC (Statistical FSC resolution estimation of cryo-EM maps) More
• SPOC (Statistical post-processing of cryo-EM maps) More
  
  

Cryo-EM software:

• FDR-FSC ( Statistical FSC resolution estimation of cryo-EM maps)https://erc-3-cloud.fz-juelich.de/FSC_Server/             (https://doi.org/10.1016/j.jsb.2020.107579)

• FDRthresholding (Statistical density thresholding of cryo-EM maps using "false discovery rate" control) https://git.embl.de/mbeckers/FDRthresholding             https://doi.org/10.1107/S2052252518014434

• LocScale (Local density scaling/sharpening of cryo-EM maps) https://git.embl.de/jakobi/LocScale (https://doi.org/10.7554/eLife.27131)

• SPOC (Statistical post-processing of cryo-EM maps) https://github.com/MaximilianBeckers/SPOC (http://dx.doi.org/10.1016/j.jsb.2020.107579)

• Spring (single-particle based helical reconstruction software suite) https://spring.fz-juelich.de https://doi.org/10.1016/j.jsb.2013.11.003

Custom-made TEM hardware components

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