Biomedical Imaging Research Unit

DAY 1 - Wednesday 22 February

9:00am Dr Carola Thoni, Lastek Pty Australia Ltd

'Introduction to STED microscopy'

Link to video

9:30am Dr Alex Fulcher, Monash Micro Imaging, Melbourne

'STED - One Ring to Resolve them All'

Link to video

Speaker's visit to BIRU funded by the Microscopy Knowledge Exchange scheme between Australia and New Zealand established in partnership with the Australian Microscopy and Microanalysis Society (AMMS) and Microscopy New Zealand (Microscopy NZ).

10:00am Dr David Crossman, BIRU Director, Dept of Physiology

'Biology at the nanoscale – calcium singalling in the heart'

Link to video

11:00am Jacqueline Ross, Biomedical Imaging Research Unit

'Real life experiences using the BIRU STED microscope'

Link to video

11:30am Dr David Baddeley, Auckland Bioengineering Institute

'Opening the black-box - what is deconvolution, how does it work, and what to look out for ...'

Link to video

DAY 2 - Thursday 23 February

9:00am Dr Gero Schlötel, Abberior Instruments GmbH, Germany

'STED: Versatile super-resolution technology ready for new approaches and challenging samples'

Link to video

Tzipi Cohen Hyams and Murray Killingsworth

Ingham Institute of Applied Medical Research, Western Sydney University (School of Medicine), UNSW Sydney, SWSCS Medicine, NSW Health Pathology

'Novel translational applications of Electron Microscopy in research and diagnostics'

Link to video

Speaker's visit to LabPlus funded by the Microscopy Knowledge Exchange scheme between Australia and New Zealand established in partnership with the Australian Microscopy and Microanalysis Society (AMMS) and Microscopy New Zealand (Microscopy NZ).

Dr Lloyd Donaldson, Forest Genetics & Biotechnology, Scion

'Confocal SRRF microscopy of plant cell walls'

Link to video

Abstract
The nanostructure of plant cell walls is of interest for food and biomaterials applications but high-resolution techniques such as electron microscopy require the sample to be dry or frozen and hence changed from the natural state. Light microscopy allows examination of cell walls in the wet state but with limited resolution. We developed a protocol for high-resolution imaging of wet cell walls using confocal microscopy and SRRF [super-resolution radial fluctuations] based super-resolution. We compared autofluorescence with acriflavin staining for lignin and rhodamine B staining for lignin/porosity visualisation. SRRF microscopy offers advantages over other super-resolution techniques in that no specialised hardware is needed and the technique can be used with any fluorescent stain as well as with autofluorescence which is particularly important for plant tissue imaging. SRRF microscopy offers advantages over other super-resolution techniques in that no specialised hardware is needed and the technique can be used with any fluorescent stain as well as with autofluorescence which is particularly important for plant tissue imaging. Images are acquired as a sequence of 100 images of the same location. These data are then processed with ImageJ software using a computer with graphics acceleration.

Jacqueline Ross, Biomedical Imaging Research Unit

'Ready, STEDy, go – first steps into STED microscopy'

Link to video

Abstract

Researchers worldwide continue to demand improvements in technology in order to answer complex biological questions including in the field of microscopy. Increasingly, higher level technology is expected to be used. Stimulated emission depletion (STED) microscopy is reported to be able to achieve lateral resolution of 20 - 50nm. An Abberior Facility Line STED microscope, funded through The University of Auckland Shared Research Infrastructure Fund, was installed in the Biomedical Imaging Research Unit last year and is available for use. Researchers who have experience with immunofluorescence labelling and other fluorescence labelling for widefield and confocal microscopy will have an advantage in using the system, however there are some changes required to specimen preparation such as fluorophore and mountant choice. Learnings from the experience to date will be reported, which should provide useful guidance to those who are interested in using the technology. Preliminary data from the system will be presented.

Image segmentation and analysis are critical steps following image acquisition. In the following webinars, BIRU staff members Jacqueline Ross and Richard Yulo each demonstrate a software package that can be used to solve some image analysis problems. Jacqui uses Fiji to explain a typical example of an image analysis pipeline, the steps involved and provides a brief introduction to the use of macros. Richard uses the Intellesis module in ZEN to show how machine learning can be used for image segmentation. Through these webinars, you will get a feel for different software interfaces and results that can be obtained from them. Ratish Kurian introduces the virtual machines that the BIRU have set up to assist users with challenging data sets that require a higher-level resource than your standard desktop PC.

Thanks to the FMHS postdoctoral society for organising this event!

1. A taste of Fiji - Jacqueline Ross 
2. Imaging IT infrastructure - Ratish Kurian 
3. Automated image segmentation using machine learning - Dr Richard Yulo