Imaging Processing Software Guides and Manuals

In addition to the software manuals listed below, our staff provides consulting on imaging and labeling methods and their applications to research; training on individual instruments, imaging systems and software; tutorials in principles and techniques of microscopy and image analysis.

Importing Image Files

Import Olympus and Slidebook Files

Describes the Fluoview and Slidebook file formats with detailed instructions on how to open in software applications such as Huygens and Fiji.

Import Bio-Rad Files

Fiji can open .PIC format used with Bio-Rad confocal microscopes. The Bio-Rad is obsolete, but the files linger.


Huygens Professional Guide (17.8 Mb)

User's manual for Huygens Professional, version 15.05. An informative manual for performing deconvolution, 3D rendering, 3D object anaylsis, colocalization and aberration correction. From Scientific Volume Imaging.

Huygens Wizard Guide.pdf (3.5 Mb)

Abbreviated guide for using the "wizard" function in Huygens Professional that walks you through the steps for deconvolution. Based on Huygens Essential, which is entirely driven by wizards.

Image Processing

Making Figures for Publication (3.1 Mb)

A tutorial on creating 3-color and 4-color images, merging grayscale with color, making multi-panel images and adding annotations for publication.
Explains the types of color images, contrast and gamma, and making scale bars. Primarily using Photoshop, but relevant to Fiji. Written by Glen MacDonald.

Translation, not Manipulation (15.5 Mb)

An overview of why image processing is necessary and the basic operations of image processing for publications and presentations. Taken from lectures given by Glen MacDonald.

Creating Movies with Fiji (970 Kb)

Creating animations in 2D and 3D, adding annotations, cropping, combining, creating insets and understanding effects of compression. Written by Glen MacDonald.

Fiji (ImageJ for Biologists)

Installing Fiji (97 Kb)

Step by step instructions guide you through a full installation of Fiji, including the most recent version of Java, plugins for file import and macros for Fiji. Note that installing macros is a bit vague since the server on which they are stored is under construction. Written by Glen MacDonald.