Imaging Software


One picture is worth ten thousand words? This is a vast understatement! Monochrome images may range from 300,000 to several million pixels! In microscopy, image analysis is used to extract meaningful information about an image’s contents. Often simple image analysis tasks for example, distinguishing an object from its background can turn out to be more difficult to accomplish than one would expect! There are several image analysis and processing software packages available to you for this purpose. Access to and advice about the following image analysis and processing software can be provided by the Bosch AMF.

We endeavor to establish an Image Analysis Suite within the Advanced Imaging Facility, that will cater to all image processing and analysis needs.

Confocal Assistant

Software for 3D analysis of confocal images. Version has not changed since 1996, but still runs well on most Windows platforms. Download version 4.2 (Windows 3.1, 95/98/NT/2000, 1.09 Mb).


Bitplane Imaris

Located on Imagingmac in Room E401, Anderson Start Building.

Imaris® is Biplane’s core software module that delivers all the necessary functionality for visualization, segmentation and interpretation of 3D and 4D microscopy datasets. Combining speed, precision and ease-of-use, Imaris provides a complete set of features for working with three- and four-dimensional multi-channel images of any size, from a few megabytes to multiple gigabytes in size. One can conveniently load, process and visualize images acquired from almost any confocal and wide field microscope in order to gain new and ground-breaking insights from your image data.

The latest Imaris® suite with the ImarisVantage upgrade is now available at the Bosch AMF. It allows spectacular 3D-rendering (Imaris) to discover relationships that may have remained hidden, tracking and analysis of cells and their components over time (ImarisTrack), measurements of protein co-localisation (ImarisColoc), tracing of fine structures (FilamentTracer) and immediate visualisation of statistical parameters of a selected object without the need to search through a separate table (MeasurementPro).

Funding for the purchase of this software was provided by Rebecca L. Cooper Medical Foundation Grant 2009, Research Infrastructure Block Grant 2008 and 2009, Anatomy and Histology, Physiology and the Bosch Institute. Funding for the upgrade including the ImarisVantage was supported by the RIBG 2012.

Imaris image

Image by Sharissa Latham.


Image Tool



Located on Imaging Mac and Imaging PC in Room E401, Anderson Stuart Building.

The Bosch AMF has recently upgraded its MetaMorph software with Ver. 7.6 and the addition of the Granularity Application Module. Researchers can now use MetaMorph's extensive analysis tools to measure areas, intensities, distances, volumes, graph intensity levels over time, segment and quantify objects, and more. All measurements can be directly logged to a text file or Microsoft® Excel. The Integrated Morphometry Analysis module allows objects to be measured and separated into user-definable classes, based on any combination of measured morphometric parameters, such as shape, size, or optical density.

The Granularity Application Module allows one to count punctate objects and is particularly designed for analysing images showing receptor internalization or clustering of target molecules. Other modules such as Count Nuclei and Multiwavelength have been installed in the MetaMorph on the Imaging Mac.

Funding for the purchase of this MetaMorph upgrade and the additional Modules was provided by Physiology, Pathology and the Bosch Institute.

MetaMorph software

NIH Image


Scion Image

Zeiss AxioVision LE

ZEN lite

ZEN lite is the free basic version of the high-performance microscopy software, ZEN. You do not need a license for ZEN lite as a viewer for your CZI files.

Available for Windows only. Download Zen 2012 for a 32 bit operating system or Zen 2 for a 64 bit operating system.

Use ZEN lite to:

  • Acquire images and simple video sequences
  • Measure distances and areas interactively
  • Open, edit and save CZI files and export into various formats
  • View meta data relating to CZI image files
  • Create basic reports