SIMCheck Logo SIMCheck download

an open source ImageJ plugin suite for super-resolution structured illumination microscopy data quality control

Quality control

  • DeltaVision OMX, Zeiss Elyra, Nikon N-SIM data format compatibility
  • Raw data intensity profile (bleaching, angle variation, intensity fluctuation)
  • Raw data Fourier analysis to assess illumination quality
  • Motion blur and angle illumination variation
  • Modulation contrast map & average modulation-contrast-to-noise ratio
  • Reconstructed data histogram analysis
  • Spherical aberration mismatch between sample and reconstruction OTF
  • XY and Z Fourier analysis to identify reconstruction artifacts and asses frequency support vs. effective resolution
  • Identification of noise reconstruction artifacts and saturated pixel
  • Log-file with results & interpretation guidelines
  • Summary statistics table
  • Online help
Calibration tools

  • Axial modulation pattern focus (top-phase calibration)
  • Phase stepping analysis

  • Synchronous xyz-cropping of raw and reconstructed datasets
  • Format converter (Zeiss Elyra / Nikon N-SIM)
  • Pseudo-widefield image generation
  • Auto-threshold & 16-bit composite TIF converter
  • Stack FFT (variable options)



Download PDF of print version plus revised supplementary material here

For further information contact: /

SIMCheck documentation and manual here

GitHub SIMCheck code on GitHub here