Coral Reef Ecology Laboratory - Professor Mark Ian McCormick

Mark McCormack Reef Fish Ecology

Student Resources

Staying abreast of recent literature

It's difficult to stay in touch with all the published research on the topics in which you are interested. Luckily JCU subscribes to "ingentaconnect InTouch" which is a referencing database that sends you the contents of your selected journals and the results of your search terms every week. All you need to do is log on and sign up at:

JCU signs up to many electronic search engines for literature. One of the most useful is the 'Web of Science'. Go through the Library website to access this database. The useful thing about this database is that it will export your search results straight into your EndNote database on your computer (or a storage area on the web). EndNote is available from the library and is a very useful bibliographic software.

As well as the above options there are also a few other routes you can take to source information. Firstly, google scholar is an extremally useful tool to quickly assimilate information,  particularIy about researchers you may be interested in. Below are the links to some of the researchers associated with the reef fish ecology lab:

Mark McCormick 

Philip Munday

Maud Ferrari

Douglas Chivers

Mark Meekan

Paolo Domenici

Shaun Killen

Steve Simpson

Many researchers also have an online presence in various social media outlets, one of which is ResearchGate. This has been touted as "Facebook for scientists" and is a great place to communicate with fellow researchers. Another useful tool is twitter. I urge all students to have a twitter account and to follow researchers they are interested in. Twitter is a fast paced information source and is a useful tool to quickly assess changes that occur in your field of interest. Follow the reef fish ecology lab page. Also worth a mention is Facebook, one of the most widely used social media platforms, this is great way to advertise your ideas and research.

Happy hunting!

Image analysis software

Image-J  Click to visit their site and obtain a download

This is really handy to do all sorts of things that we as ecologists need to do. It'll calculate areas or distances from aerial photos, egg densities in photos of egg clutches and even will allow us to obtain burst speeds from high speed video. One of the best things it is freeware!

Image-J can display, edit, analyze, process, save and print 8-bit, 16-bit and 32-bit images. It can read many image formats including TIFF, GIF, JPEG, BMP, DICOM, FITS and "raw". It supports "stacks", a series of images that share a single window. It is multithreaded, so time-consuming operations such as image file reading can be performed in parallel with other operations.

It can calculate area and pixel value statistics of user-defined selections. It can measure distances and angles. It can create density histograms and line profile plots. It supports standard image processing functions such as contrast manipulation, sharpening, smoothing, edge detection and median filtering.


Optimas 6.5 Basic instruction guide  click here for a short guide

Optimas is image analysis software that does similar things to Image-J, but has some nice additional features that make it useful for obtaining increment widths from otolith cross sections.


Photomicroscope instruction guide   click for a short guide

This is a guide to the photomicroscope in rm 167 of the Old Biology Building JCU

Otolith processing manuals

Like it or not, we can learn a lot about fish of every size by looking at the internal structure and the shape of their earstones or otoliths

This is a link to a number of manuals that will give you an initial idea of how to process them. Be aware that most of these talk about using diamond saws and their are much easier and low tech ways of process the otoliths for annual or daily rings. For large otoliths, you can't beat a diamond saw.

Click here to be re-directed to Iain Suthers' lab for otolith manuals. If you have problems downloading them, come and see me for a copy.


How we process otoliths  click for quick guide

It's always good to know how other people do things, and this is how we have been processing most of our sagittal otoliths from coral reef fishes (juveniles and adults)


Marine and Aquaculture Research Facilities Unit (MARFU)
The Aquarium Complex

Research and user protocol  click for guide

Researcher application for use  click for Word doc


Volunteer website

If you need a volunteer for field or laboratory work, then you may find one at the following address. This is managed by the Teaching Resource Centre in Biological Sciences.

click here


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