1 Live and fixed cell super-resolution imaging with Elyra 7 and Lattice SIM.

Date: 18/08/2021
Time: 1:30pm – 5.00pm

Brief Description

This workshop will give researchers the opportunity to experience the latest developments in the field of super-resolution microscopy. Lattice SIM provides researchers with the opportunity to explore biological systems in more detail, but at the same time do so in a more gentle way, certainly compared with previous SIM solutions and other technologies like STED and Single molecule imaging.

This will be an online workshop

Contact: Gavin Symonds and Dr Elvis Pandzic
(gavin.symonds@zeiss.com; e.pandzic@unsw.edu.au)

2 Live cell volume imaging with the ZEISS Lattice Lightsheet 7

Date: 16/08/2021
Time: 1:30pm – 5:00pm

Brief Description
Gain some insights into new lattice lightsheet technology and how this can be used to image live cells over very long time scales, very gently and in enough detail and resolution to see the dynamic behaviour of your biological system. An introduction to the lattice lightsheet concept is followed by (remote) hands on exposure with the new ZEISS Lattice Lightsheet 7 volume imaging system.

This will be an online workshop

Contact: Gavin Symonds and Dr Sandra Fok
(gavin.symonds@zeiss.com; sandra.fok@unsw.edu.au)

3 Imaging in Neuroscience – A Virtual Conference

Dates: 7-8 July 2021

Brief Description
This two-day event features a number of invited speakers including Dr Zhi-yong Shao and Dr Homaira Nawabi discussing some of the latest developments within neuroscience. Topics include the formation and maintenance of neuronal circuits, to developing our understanding of neuronal disorders and their treatment. Techniques that have become so useful to neuroscience studies such as clearing and optogenetics will also be covered. The range of live talks are backed up with on-demand talks and will ensure plenty of opportunity for interaction and discussion.

4 Correlative and multimodal microscopy at the micro, meso and nanoscales.

Date: 20/08/2021
Time: 1:00pm – 5:00pm

Brief Description
This will be an online half day course that will focus on highlighting workflows, equipment and applications in the correlative microscopy space. It will primarily focus on correlation between light and electron beams but will also feature other microscopy modalities including micro-CT and AFM. The course will run as a series of seminars that will feature practical components of the workflows, feature pre-recorded practical demonstrations of data acquisitions and highlight the application of these techniques. Each speaker will be given 45min to present with question time at the end of each session.

This will be an online workshop and will be limited to 20 people.

Contact: Dr Nicholas Ariotti, Dr Joanna Richmond
(n.ariotti@unsw.edu.au; joanna.richmond@unsw.edu.au)

5 Image Analysis with Python.

Date: 09/08/2021
Time: 1:00pm – 6:00pm

Brief Description
The use of Python in science has exploded in the past decade, driven by excellent scientific computing libraries such as NumPy, SciPy, and pandas. In this tutorial, we will explore some of the most critical Python libraries for scientific computing on images, by walking through fundamental bioimage analysis applications of linear filtering (aka convolutions), segmentation, and object measurement, leveraging the Napari viewer for interactive visualisation and processing. We will also demonstrate how to extend these concepts to large images with Dask and using deep learning libraries such as Stardist and Cellpose.

The tutorial will consist of mixed lectures and exercises. The material will cover the following topics:
-image filtering (scipy.ndimage.convolve)
-visualization in napari (napari.Viewer)
-image segmentation (skimage.segmentation.watershed, cellpose, stardist)
-object properties (skimage.measure.regionprops)
-large images (dask.array)

This will be an online workshop and will be limited to 30 people.

Contact: Dr Pamela Young

6 Leica TauSense integrated fluorescence lifetime information: adding extra dimension to routine imaging workflows.

Date: 19/08/2021
Time: 10:00am – 4:00pm

Brief Description
Leica Microsystems and Microbial Imaging Facility at University of Technology Sydney collaborate to demonstrate TauSense lifetime imaging on a STELLARIS 8. In addition, a THUNDER live cell imager will be onsite to demonstrate workflow efficiency between the two modalities of widefield and confocal.

This will be an online workshop and will be limited to 16 people.

Contact: A/Prof Louise Cole and Scott Merrington
(louise.cole@uts.edu.au; scott.merrington@leica-microsystems.com)

7 MATRIX STED – Many eyes see clearer: enhancing signal quality and brightness.

Date: 03/08/2021
Time: 3:00pm – 4:00pm

Brief Description
We present and demonstrate an array-based detector: the Matrix detector. We show the improvement of the signal to background ratio of STED images in biological relevant samples.

This will be an online workshop and will be limited to 50 people.

Contact: Dr Carola Thoni

8 Introduction to fluorescence temporal and spatial correlation spectroscopy: tools to quantify molecular diffusion, flow and densities in situ.

Date: 16/08/2021
Time: 9:30am – 12:00pm

Brief Description
This workshop introduces the participants to a suite of tools that can be used to quantify the microscopy images, in order to extract molecular or organellar properties, such as dynamics, co-localisation, binding kinetics and density.
The participants will be exposed to the underlying principles of fluorescence fluctuation correlation spectroscopy and how the fluctuation of fluorescence as captured in different dimension (space and time) of modern fluorescence microscopes, can be exploited to quantify information about molecules in cells. Workshop starts with a brief introductory talk and follows with hands on exercises, where participants will be able to simulate microscopy data and apply various FFCS tools to recover simulated parameters. This workshop is based on the manuscript : E. Pandzic and R.M. Whan, A Practical Guide to Fluorescence Temporal and Spatial Correlation Spectroscopy, The Biophysicist (2021) 2 (1): 40–69

Pre-requisite: Each participant will have to install the Matlab and download the scripts from the manuscripts below (in supplementary section). Please add the scripts to the path of Matlab as shown in Fig 2 of the manuscript. If any participant is unable to access Matlab and complete these pre-requisites, it is still encouraged to do it post-workshop, and just join for the demonstration. Please consult the section III of the reference manuscript for more details of how to prepare scripts for workshop. Also, have a copy of manuscript with you for reference as it will be used in the demonstrations section of this workshop.

This will be an online workshop and will be limited to 20 people.

Contact: Dr Elvis Pandzic

9 Introduction to OPAL multiplex immunohistochemsity

Date: 17/08/2021
Time: 3:00pm – 5:00pm

Brief description
OPAL multiplex staining enables the analysis of up to 8 protein markers in a tissue sample at single cell resolution. This workshop is designed for researchers who are new to the OPAL technology and will provide attendees with the background on how OPAL staining works and how to develop panels, perform staining, acquire data, and analyse data.

This will be an online workshop and will be limited to 50 people.

Contact: Dr Paul McMillan

10 Livecyte: Uncovering the inconvenient truth behind manual cell trackingy

Date: 17/08/2021
Time: 10:00am – 1:00pm

Brief description
Manual tracking using a point and click system is the most common method for measuring motility of multiple cells over long periods of time. It requires imaging techniques with very low phototoxicity therefore conventionally techniques dependent on high contrast images (as seen in fluorescence) are used, but these modalities are poorly suited to automated cell identification. Thus many researchers are forced to track cell motion by hand in order to understand their migratory behaviour. Manual tracking deployed throughout the time lapse, is time and labour intensive, suffers from inter-operator variability, ill-defined cell centroid positioning, and an intrinsic lack of morphological data. In many cases, the vast number of cell images collected during a time-lapse means only a subset of cells are tracked within a population leading to a poor approximation of migration rates. Manually tracking cells is not as accurate as people assume and significant variability can occur from person to person, therefore a more a sophisticated solution is needed.

Join us for our workshop series which includes three half hour webinars.
1/ Measuring random motility and wound healing with Livecyte: Are you only scratching the surface? (time 10.00-10.30am)
2/ Multiplication and division: Calculating growth and proliferation at population and single level with Livecyte. (time 11am-11.30am)
3/ Fluorescence in QPI Imaging: The mCherry on Top. (time 12noon-12.30pm)

We will illustrate and understand the root causes of manual tracking inaccuracies on a fundamental level and how using computer algorithms can eliminate them. Such automation has the added benefits of substantial time savings and removing the subjective nature of human interaction. We will demonstrate the Livecyte system, which is currently installed and ready for use within the UNSW. Using ptychography, a quantitative phase imaging modality, Livecyte is both ideally suited to label-free automated single cell tracking and extremely low phototoxicity.

This will be an online workshop.

Contact: Peter Davis

11 Australian Bioimage Analysis kickoff event

Date: 20/08/2021
Time: 2:00pm – 4:00pm

Brief description
Image analysis is a growing field in Australia, with a unique set of interests, tools, approaches, and challenges. In this 2-hour interactive workshop, attendees will get to know other image analysts from around the country: From what it means to be a career image analyst, to how image analysts are seen and recognized by the life science community, to actions we can take to drive growth in this field in Australia and enhance our community of practice as a whole. We will also look at examples of such communities in Europe and Melbourne, and discuss plans for setting up a national image analysis meeting group in Australia more broadly.

This will be an online workshop.

Contact: Dr Greg Bass

12 Explore large multi-channel and time series data with Amira Software and the new Xplore5D extension.

Date: 10/08/2021
Time: 10:00am – 11:00am

Brief description
This presentation will focus on the visualization and image processing of large 3D data using the new capabilities of Thermo Scientific™ Amira™ Software. This workshop will give you the possibility to learn, through a step-by-step demo, the recently added functions of Amira Software’s new Xplore5D extension. Xplore5D offers fast and easy exploration of large multi-channel and time series imaging data. We will also highlight and demonstrate Deep-Learning based training and prediction modules.

Contact: Danna Li, Product Application Specialist, Thermo Fisher Scientific
( danna.li@thermofisher.com )