Stacks Image 1284

Divisional Research Infrastructure Governance Group (DRIGG)


As many of you may be aware, the OCCM is no longer administered by the Department of Anatomy, but has become part of the DRIGG. Along with the OCEM, Histology Unit, and FACS the OCCM forms part of an imaging subgroup within the greater DRIGG.

As the OCCM is now administered by Health Sciences at the Divisional level, there are a number of changes to be aware of:

All Division of Health Science departments will be charged at the same hourly rate.

All Division of Science departments will be charged at four times the Health Sciences’ rate.

Division of Sciences’ users are encouraged to discuss their funding options with their Head’s of Department.

Please contact Andrew McNaughton for further details if you have questions regarding how this might affect your research.
Stacks Image 1831
Stacks Image 1834
Stacks Image 1835
Stacks Image 1836
Stacks Image 1837
Stacks Image 1838
Stacks Image 1839
Stacks Image 1840
Stacks Image 1841
Machine Learning using Ilastik

The links to the left will take you to the Ilastik website, or to a specific topic.
The program is under quite rapid development, so check back to see if other features have been added.
IlastikWhere to start and get a feel for what it can do, a few specific examples are linked below to get you started.
Pixel ClassificationThe workflow is especially suited if the objects of interests are visually (brightness, color, texture) distinct from their surrounding. The algorithm is applicable for a wide range of segmentation problems that fulfil these properties.
CarvingThis is suited to greyscale images which do not exhibit clearly delineated intensity zones, but have features separated by boundaries. TEM images, both 2D and 3D are good candidates for this method.
Animal Tracking
Digitally label animals in mazes and track/quantify where and when they go.

Confocal: How it Works

For most biological samples, a fluorescent marker(s) is required to use the confocal microscope.

Generally, if you've successfully stained your samples and viewed the results under an ordinary epi-fluorescence microscope, your samples will be suitable for the confocal. In other words, you've already done 90% of what's required.

Light Microscopy

We have a number of research grade light microscopes available for use. Most also have epi-fluorescence as well as bright field capabilities.

Other, more specialised microscopes, can obtain montages of large specimens or help you with stereology investigations.

Fiji and Analysis

Open source software. like ImageJ, can provide an excellent platform to base image analysis upon. There's a lot more to simply obtaining a 'pretty picture' with any of the equipment listed here.

You should be able to at least make semi-quantitative assessments of the data you have collected. This is where image analysis come in.

µCT: Sample Suitability

The µCT uses Computerised Axial Tomography (CAT) to produce a series of digital slices of solid objects. Best suited to relatively dense material like teeth and bone, the µCT can resolve details down to about 1µm.
If you're looking for electron microscopy techniques, go here: OCEM

Contact Details

Andrew McNaughton
03 479 7308
andrew.mcnaughton@otago.ac.nz

Room B01g Basement
Department of Anatomy
Lindo Ferguson Building
270 Great King Street
(Opposite main entrance to Public Hospital, Great King Street)
PO Box 913
Dunedin 9001
New Zealand