Biomedical Imaging Research Unit

These documents were created by Jacqueline Ross for an image analysis workshop held during the 28th New Zealand Conference on Microscopy on 31 January 2017. The version used was the latest stable build available at the time and all additional plugins were installed for workshop participants who received a USB with complete versions for Mac and Windows. Where it is necessary to download an additional plugin, e.g. Biovoxxel toolbox or Angiogenesis Analyzer, the documentation contains a link. The images used for the workshop cannot be supplied without permission from the owners.

The workshop was intended as a beginners workshop to get people started in using Fiji for image processing and analysis purposes so is focused on answering the most common analysis/processing questions. Once the necessary steps have been identified, it is usually straightforward to create a macro to batch process/analyze the images. There are a couple of examples of the use of macros to demonstrate how powerful the software can be.

Please note that the software should be cited in all publications according to the advice given here.

An acknowledgement to the creator of the documents would be greatly appreciated in any publications that are significantly progressed by the use of this documentation. Authors of specialised plugins should be acknowledged and any publications associated with these should be referenced. Please do not change these documents without permission or upload them to any alternative sites as they are covered by copyright.