Department of Medicine

Indiana Center for Biological Microscopy

Software for Image Analysis

Imaris, provides a clean and straight forward way of segmenting and quantifying objects of interest in 3D and with time.  The software provides a plethora of 3D quantifications characterizing cell and object shapes, intensities and colocalizations. In addition Imaris can perform a variety of time based analyses.  Contact Gosia or Mary for an introduction to this powerful new package and an explanation of its various tools and capabilities.


Metamorph v7, is a useful software package that implements a variety of image analysis and visualization tools.  It employs numerous built-in image analysis routines to address common protocols including: segmentation, colocalization, and FRET analysis.  The visualization tools include standard manipulation and basic 3D rendering of image stacks from confocal microscopes.  This package is available on both imaging stations.

Amira v4.5, is a powerful manual segmentation and visualization tool with an exceptional learning curve.  Please contact a Center staff member to assist in its use.  This package is available on Imaging Station4.

Free software for image analysis:

The microscope softwares used in the core generate a variety of image formats.  Each manufacturer provides tools for opening, adjusting and exporting these files.  As an alternative, the open source software ImageJ/Fiji implements a file reader that will open all of these files and well as the associated capture information.

               Olympus.  Windows.  Olympus FV10-ASW 3.0 Viewer. (contact us)

               Nikon. Windows and OSX. NIS Viewer.

               Leica. Windows. LASAF lite.

               Zeiss. Windows.  LSM Image Browser.

Open source software for image analysis:

ImageJ or Fiji. These open source image analysis and visualization software packages can be freely downloaded.  Both packages implement a large variety of standard processing tools as well as some novel analytical tools.  As an open source platform, end-users have access to the code for verification and customization of tools.  The Center has extensive experience with custom processing and analysis workflows in ImageJ and development of macros tools and novel analytical approaches implemented in the ImageJ plugin framework.  For more information contact us.

Useful plugins and macros. Coming soon!

Free software developed by the Center:

IMART – Intravital Motion Artifact Reduction Tool – Software designed to correct motion artifacts in sequences of images collected in intravital microscopy, in time series or in three dimensions. Developed by Kevin Lorenz and Edward Delp (Purdue University) and Paul Salama (IUPUI), IMART software is available for free download, and can be obtained by sending a email request to

Voxx. A voxel-based 3D imaging program developed by Jeff Clendenon and Jason Byars that is capable of near real-time rendering of large microscopy data sets on inexpensive personal computers.