Bioimage Analysis Core

The Bioimage Analysis Core (BAC) is a team of dedicated image analysts whose role is to assist researchers at WEHI and external collaborators in extracting the most information possible from their microscopy datasets.

Established in 2019, the BAC is the first of its kind in Australia. It provides access to a wide range of data visualisation and analysis tools, training and powerful computational resources, and most importantly access to a team of highly specialised analysts to help process increasingly complex imaging data.

Online booking

Cells are imaged in a monolayer with several markers. They are then segmented and classified using a variety of measured properties that can be individually adjusted depending on the cells of interest. Credit: Tan Ngyuen, Ken Pang, Lachlan Whitehead

Areas between vessels in the retina can be used as a descriptor of retinal abnormality. Randomized colours are often used as a quick way to check the accuracy of the segmentation. Credit: Leigh Coultas, Lachlan Whitehead

Hardware

The BAC provides access to a staggering amount of computational resources. Leveraging WEHI’s High Performance Computing Cluster, the BAC hosts a suite of virtual machines (VMs) with large amounts of RAM for efficient image processing. High-end GPUs offer high-level performance when visualising multidimensional datasets, but also provide a strong basis for AI-assisted analysis tasks.

All the computational resources of the BAC are accessed remotely and can be booked online, allowing the institute’s scientists to have secure access to their data and compute from wherever they happen to be.

Software

The BAC’s staff have extensive experience in a range of open-source and proprietary software for image analysis,offering support and the development of pipelines across multiple platforms, including:

FIJI
Qupath
Python and Napari
Ilastik
Imaris
Arivis
Aivia

The BAC also provides access to a Virtual Reality headset and Syglass software allowing researchers to visualise and annotate their data from the inside-out.

Along with the institute’s ITS and Research Computing Platform, the BAC also hosts an instance of OMERO – the open-source image management database, allowing researchers to view, organise, analyse and share data from anywhere with internet access.

Dr Lachlan Whitehead

Dr Pradeep Rajasekhar

Ishrat Zaman

Contact the Centre for Dynamic Imaging to book equipment or discuss imaging collaborations.

imaging@wehi.edu.au