Surface2SurfaceDists_NNeighbors is an Imaris extension that calculates the distances from every surface within a Surface object (reference surface) to every surface within a different Surface Object (target surface). Additionally, this extension finds the number of nearest neighbor target surfaces from a reference surface within a user specified search radius (µm). The output results are saved to an excel spreadsheet. If the data set has time points, each time point is saved as an additional Sheet in Excel.;

  • Imaris 9.2.1
  • Microsoft Excel
  • Matlab 2014 or newer    


  • Download at GitHub.
  • Place the contents of the .zip file into your default Imaris extensions folder.
  • Within the Imaris software, click Edit > Preferences > Custom Tools.
  • Within Custom Tools click the 'Add' button and navigate to the matlab directory where the sortomato contents were placed.
  • Click 'Select Folder'.    


  • Make a folder.
  • Unzip the zip file and copy the contents (should be 3 files: Surface2SurfaceDists_NNeighbors.exe, Surface2SurfaceDists_NNeighbors.xml., ImarisLib.jar) into your new folder.  
  • In Imaris, go to File > Preferences and click on the 'Custom Tools' tab.  
  • In the Xtension Folders pane, click 'Add...'  
  • Navigate to where your Surface2SurfaceDists_NNeighbors executable and XML file are and click 'OK'.  
  • Click 'OK' to exit the Custom Tools tab.      

Matlab Runtime Compiler:   

Executing the XTension   

Once you have executed Surface2SurfaceDists_NNeighbors, four pop-up windows will show up. 

  • Choose the 'reference' surface population.
  • Choose the 'target' surface population.
  • Enter a search radius (relative to the reference objects). 
  • Choose a path and filename for the output Excel file.