Image Analysis

University of Otago Logo

Almost all of the data produced at Microscopy Otago is in the form of images. How this is analysed can make a dramatic difference to the conclusions drawn from the data. We offer a range of expertise in image analysis as well as the techniques needed to acquire reliable images from the equipment.

Analysis Programs

This is not the end of all lists, it only indicates the common programs used by the staff and which they can offer first hand help in the use of. If you require assistance in other programs don't hesitate to ask as learning goes both ways if you tell us of new programs or methods.



IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files.

IMOD was developed at the Boulder Laboratory for 3-D Electron Microscopy of Cells and is open source software so is free to download and use on your laptop. It has also been installed on the OCEM computers.

Image J

One of the more underrated programs, Image J is the cross platform evolution of NIH Image. It can be expanded by installing any of the vast array of plugins and macros, which like the program itself are offered freely courtesy of the open source software principle. Details of Image J can be found at Image J

University of Otago Logo

Image J is very good for measuring length, area, thresholding regions of interest and extracting numerous other parameters from your image data. It will open most file formats, including proprietory formats used on confocal microscopes.



Avizo (previously known as Amira) is state-of-the-art industry software that is particularly useful for analyzing 3D data sets. It has a 'skeletonisation' add-in that statistically analyses the connectivity of networks. Some uses could include the permeability and percolation of geological samples, or how blood flows in biological specimens.

Avizo is available to use on the OCEM's MacPro. For more information about Avizo contact Dr. Virginia Toy (Department of Geology).


Amira is a high end 3D reconstruction and analysis program, particularly useful for ÁCT data and confocal images. 'High end' is a euphemism for 'it will take you a long time to use it to its full capacity'. Details of Amira can be found at Amira

University of Otago Logo

Amira is worth the effort to learn if 3D modelling is what you need to do, simple isosurface reconstructions are relatively easy and can be produced with a few hours of practice. How difficult more demanding reconstructions will take often depends upon the quality of data you are working with. This is true of any analysis program but can be particularly painful when extracting relevavant data from large 3D volumes.

Amira is not a free program and to use it requires purchasing a licence for some thousands of dollars (Mac or PC versions), or ... using the copy we have at Microscopy Otago. If you are thinking of using this software contact Andrew McNaughton for further information.


University of Otago Logo

This is a program written for the CT medical market, but it offers many useful features for microscopy and ÁCT data. Details of Osirix can be found at Osirix

An advantage of Osirix is it can do both 2D and 3D analysis in the one program. Slice data can be viewed and analysed as single images or data can be viewed and digitally resliced to broaden the analysis further.

Osirix will only run on a Macintosh computer so there's another good reason to switch over. The other plus is it's free but a 64 bit version for making full use of RAM with large data sets is available for $US169. If you are thinking of using this software contact Andrew McNaughton for further information.

Serial EM

serial em

SerialEM is a program that can acquire a variety of data from electron microscopes: tilt series for electron tomography, large image areas for 3-D reconstruction from serial sections, and images for reconstruction of macromolecules by single-particle methods. This software is installed on the computer for use with the JEOL 2200FS Cryo-TEM.