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General Information

ScanImage 5.1  is software for linear or resonant two-photon laser-scanning microscopy.  

ScanImage supports numerous microscope platforms and is built on the same flexible acquisition hardware as our public release ScanImage 5.

  • step & settle FastZ mode, e.g. suited for Optotune electrically tunable lenses
  • auxiliary triggers for timestamping external events (e.g. behavior events)
  • syncing of acquisition to laser clock
  • semi-automated bidirectional scan alignment
  • features from ScanImage 3.8.1 including Display Striping, Power-Box and Cycle-Mode

Contact for any questions.

Upgrading Information

Unless specifically noted (as indicated by a compatibility note), upgrading from an older release of ScanImage 5.1 to a newer build will not break compatibility with Machine Data Files, User files, Configuration files, or TIFF headers. ScanImage can be upgraded by deleting the contents of the scanimage installation directory and copying in the new contents of the zip download. It may be useful to keep a backup of the old installation directory.


When upgrading to a new release of ScanImage, a location outside the installation directory can be specified to make upgrading ScanImage and backing up the complete configuration easier. It is highly recommended to move the saving location. You can do so with the following steps:

  1. Add the following code to the first (%% ScanImage) section of your Machine Data File:

    The default setting will store the files where the MDF is saved in a sub directory called ConfigData.

  2. Move the old configuration data to the new location by copying the files are listed below to the new directory. Your particular installation may or may not include each of these files:
    1. [ScanImage Installation Directory]\+scanimage\+components\+scan2d\private\ResScan_classData.mat
    2. [ScanImage Installation Directory]\+scanimage\+components\+scan2d\private\LinScan_classData.mat
    3. [ScanImage Installation Directory]\+scanimage\+components\private\Photostim_classData.mat

Version Notes

March Release (10 March 2016)

  • Support for NI-DAQmx 15.5
  • Several bugfixes and performance improvements in LinScan
  • Fixes for openTif

November Release (22 January 2016)

  • Compatibility Note for Thorlabs BScope 2 users
  • Support for Thorlabs MCM3000, USB PMT2100, USB BCM
  • Support for higher sampling rates on certain DAQs in LinScan
  • Fix powerbox with P-Z adjustment
  • Improve performance of opentif
  • Improved automatic scan phase adjustment for ResScan
  • Automatic scan phase adjustment for LinScan
  • New NI VISA interface
  • Fix several bugs in LinScan

October Release (19 October 2015)

  • Performance enhancements to acquisition starting

  • Performance enhancements to loading of usr and cfg files

  • Option to keep resonant scanner on when no acquisition is active

  • Improved linear scanning waveform with settling within fill fraction

  • Support for DAQmx 15.0.x

  • Remove TIFF header and footer size limitations

  • Fix panning channel display in Matlab 2014b and newer

  • Fix scroll wheel functionality in Matlab 2014b and newer

  • Fix issue where footer is only attached to last TIFF in acquisition

  • Updated Thor B-Scope2 support for new stage controller firmware
  • Fix issue causing acquisition to randomly stop with a data corruption error
  • Fix for Thor ECU1 component trigger routing
  • Flexible opentif
  • Linear scanning
  • Improved stability


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