Image Explorer for ScanImage

Visualization of time-varying fluorescence

Image Explorer is a data visualization tool for 3D image stacks. It includes tools for navigating and selecting images, signal playback, image contrast controls, max projection, and for visualizing time-varying fluorescence data by mousing over different areas of an image stack.

ScanImage tiffs

Image Explorer includes a loader designed specifically for loading complex .tif formats produced by ScanImage microscopy software. Although only ScanImage files can be loaded, the visualization tools will work on any 3D wave, as long as it is in the expected folder structure within Igor. See the header in the .ipf file for instructions on use, etc. 

There are likely some imaging configurations that will fail to load properly, however the following configurations of time-varying frame scans are currently supported:

  • Multiple channels
  • Multiple scan fields
  • Multiple z positions (e.g. using fast-z functionality from an electrically tunable lens (ETL) or a lens with a piezo-electric actuator
  • Z stacks with multiple frames per z position 

ScanImage interleaves channels, scan fields, and z positions in its .tif specification, so Image Explorer's primary job is to separate that data into multiple output waves for the user. 

ROI Creation

Image Explorer is capable of defining regions of interest for further analysis. Currently those ROI boundaries are saved in root:Packages:NeuroToolsPlus:ScanImage:ROIs for the user to then do what they want with them. Future updates will probably allow automatic fluorescence extraction of ROIs. This is already a feature of the NeuroTools analysis package (with ScanImage add-on package installed), so that is currently the better option for subsequent analysis using ROIs. 

Using Image Explorer

ImageExplorer.ipf goes in User Procedures or Igor Procedures.

Open Image Explorer through the 'Analysis' menu in Igor.

Important note:  Image Explorer requires the JSON xop provided by byte-physics (, so this must also be installed

Project Details

Current Project Release

Release File: ImageExplorer.ipf (188.27 KB)
Version Date:
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