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ScanImage 5 is software for resonant two-photon laser scanning microscopy, allowing cellular resolution brain imaging at the rate of behavior (30Hz and beyond).

ScanImage 5 and subsequent releases are designed to support customization layers for both CPU and FPGA-based processing which can be used to implement online or real-time analysis, including closed-loop experiments.

See Supported Microscope Hardware to begin setting up a ScanImage 5 compatible microscope system. 

Upgrading SI4 to SI5


Technical Solution exists for current ScanImage 4.x users to maximally use their existing hardware under ScanImage 5

SI5 is largely equivalent to SI4 feature-wise, plus the following enhancements:

  • Support for flexible hardware - from OEM components, to kits or systems from Sutter, Scientifica, or Thorlabs
  • Precise FPGA-based timestamps (sub-microsecond resolution) stored for each individual frame
  • Precise timestamps for each external trigger signal during LOOP acquisitions, stored to individual frame file header
  • Automatic input channel offset correction for each GRAB/LOOP acquisition is fast & seamless
  • Continuous zoom control (compared to discrete allowed values in SI4)
  • Fast external retriggering
  • More precise beam timing relative to each scanner period
  • Fill fraction no longer affects scanned area aspect ratio
  • Simplified wiring, leveraging the internal trigger routing capabilities of the PXI platform




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