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OertnerLabSpecials

ScanImage (public release, version SI55R1) is a flexible software for operating laser scanning microscopes. For some applications you might want to customize the software.

Alternating beam scanning

ScanImage can control two laser lines, however, spectral overlap of fluorophores impedes multiplexed excitation and detection. A technically straightforward solution is to alternate between excitation wavelengths in a frame-by-frame manner ("alternating beam scanning") so that an image stack with interleaved emission data is created (two channels per frame, two channels per optical section).

Setup
  • Add "OertnerLabSpecials" directory to Matlab search path.
  • Replace ScanImage function "calcStreamingBuffer" (part of ScanImage\+scanimage\+components\Beams.m, around line 1180) with the code given in "Beams-calcStreamingBuffer_modified.m".
  • Start OertnerLabSpecials from Matlab command line.
  • Set Frames=2 in ScanImage "Main Controls" window (all other params as required).
  • Activate "Enable Power Box" in ScanImage "Power Controls" (it is not necessary to set a power box).
  • Activate "Alternating Beam Scanning" in "OertnerLabSpecials". Set individual power values.
  • Run acquisition (alternating beam scanning is active in Grab and Loop mode).