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University of Birmingham
Tuesday 12th (09:00) - Wednesday 13th March 2019 (17:00)

In case of queries please contact Sharmaine Afferion:
Telephone: 0121 4148739


Registration URL

COMPARE Workshop on Single-Molecule imaging and spectroscopy of membrane proteins
March 12th – 13th 2019
University of Birmingham

We are very pleased to announce our 2019 COMPARE Workshop, which this year will focus on Single-Molecule Imaging & Spectroscopy of Membrane Proteins.

Single-molecule microscopy and spectroscopy are very powerful techniques that allow investigating the organization and dynamics of membrane proteins in cells and tissues with unpreceded spatiotemporal resolution. This workshop will bring together world leaders in single-molecule imaging and spectroscopy to focus on key questions about the spatiotemporal organization of receptors and other signalling proteins in nanodomains on the plasma membrane.

Day 1 - Tuesday 12th March 2019

A first day of talks covering both recent exciting biological findings and new methodological developments will be followed on day two by unique practical sessions. These will include in-depth demonstrations of cutting-edge single-molecule microscopy and spectroscopy techniques in collaboration with leading microscopy vendors as well as of new open source software for the analysis of spectroscopy and single-molecule data.

Confirmed speakers include
Stephen Briddon, University of Nottingham
Susan Cox, King's College London
Sian Culley, University College London
Juliette Griffie, EPFL
Benjamin Compans, King's College London
Florian Levet, University of Bordeaux
Emmanuel Margeat, CNRS Montpellier
Carlo Manzo, Universtat de Vic
Jean-Baptiste Masson, Institut Pasteur
Annemiek van Spriel, Radboudumc

Day 2 - Wednesday 13th March 2019
Venue: The Imaging Suite, Institute of Biomedical Research, Medical School

Attendees can choose up to 5 workshops for day 2 (maximum of 3 microscopy workshops).

Microscopy based workshops

Workshop 1: Using N-STORM for Single Molecule Location Microscopy.
Hardware: NIKON N-STORM.
Microscopy Specialist: Kate Lewis, NIKON.
Overview: This workshop will focus on the using the NIKON N-STORM system for Single Molecule Location Microscopy. 2D and 3D single molecule acquisition and analysis will be demonstrated.

Workshop 2: Spinning TIRF for Simultaneous Multi-Channel Single Molecule Imaging.
Hardware: Cairn Quad TIRF.
Microscopy Specialist: Martyn Reynolds, Cairn.
Overview: The Cairn TIRF system on demo is configured with a fast scanning TIRF/HILO head for excitation with detection from up to four cameras simultaneously. We will walk through the use of the Cairn spinning TIRF system and use the resulting high uniformity illumination for quantitative TIRF imaging, followed by a demonstration of single molecule localization approaches, including single particle tracking, that can benefit from the spinning TIRF approach.

Workshop 3: Evaluating Scientific Cameras for Single Molecule.
Hardware: Photometrics CMOS and EMCCDs, NIKON Ti2 Eclipse, Cairn TwinCam.
Microscopy Specialist: Louis Keal, Photometrics.
Overview: Learn more about how to evaluate camera technology for single-molecule imaging applications. We’ll also be performing a live comparison between back-illuminated CMOS cameras and EMCCD cameras to demonstrate their effectiveness for low light imaging.

Workshop 4: The Nanoimager: A demonstration of single-molecule localization microscopy carried out on a desktop compatible super-resolution microscope.
Hardware: The Nanoimager
Microscopy Specialist: Siobhán King, ONI.
Overview: A workshop on ONI’s Nanoimager offering various modes of operation including single-molecule localization microscopy (SMLM), TIRF, smFRET, smTracking, dSTORM and PALM. We will provide a brief overview of the Nanoimager and its applications in single-molecule localization microscopy and invite you to test out the system with your own samples.

Workshop 5: Application of FCS and FCS to investigate receptor dynamics.
Hardware: Zeiss LSM780.
Microscopy Specialist: Nick Sergent, Zeiss.
Overview: This workshop will give an introduction into the background of FCS and FCCS, followed by a live demonstration of technique to probe molecular diffusion and interactions.

Software workshop 1: Coordinate-based quantification of 1- and 2-colors single-molecule localization microscopy data.
Developer: Florian Levet
Overview: In this workshop we will present various analytical methods designed to quantify single-molecule localization microscopy (SMLM) data directly from the localization coordinates. It will focus on various freely available methods (DBSCAN, CBC, Clus-Doc, Voronoï-based quantifications, K-Ripley’s function, etc.), presented in the framework of SR-Tesseler ( We will discuss the pros and the cons of the presented methods by summarizing their capabilities. It aims at guiding users for choosing the most appropriate methods to their problem, whether it be for structural or colocalization analysis. As a support, we will use simulation and experimental data.

Software workshop 2: Image Quality Assessment with NanoJ-SQUIRREL: Data Preparation, Running the Software and Interpreting the Results
Developer: Sian Culley
Overview: Further details can be found at

Software workshop 3: HAWK analysis of localisation microcroscopy data
Developer: Susan Cox
Overview: HAWK analysis allows localisation data to be analysed with confidence that the results will not contain artifacts. This workshop will cover the details of what HAWK analysis does and practical demonstrations of the results it gives on different data of varying quality. Participants are welcome to bring their own data to analyse during the workshop.

Software workshop 4: The TRamWAy Python library: inferring maps of local diffusivity and force from single molecule trajectories
Developer: Francois Laurent
Overview: After an introduction on Bayesian inference of single molecule dynamics, we will install the TRamWAy open-source library from GitHub (available at and run standard use cases in Jupyter notebooks, including:
- loading simulated and experimental sets of trajectories,
- segmenting space and time,
- generating and visualizing maps of dynamical parameters such as diffusivity and force,
- determining the significance of a force using a Bayes factor technique.
We will face several limiting experimental conditions and give some guidance.

Software workshop 5: RSMLM: An R-package for pointillist based analysis of single molecule localization microscopy data
Developer: Jeremy Pike
Overview: This workshop will use Jupyter notebooks to introduce RSMLM. This R package allows users to easily and efficiently design customised analysis workflows for high throughput and efficient analysis of complex 2D and 3D single molecule datasets. We will cover commonly used cluster analysis techniques as well as more advanced methods for quantifying the shape or topology of biological nano-structure. For more details see our pre-print:

To register for this event, please visit the University of Birmingham Shop
Registrations can be made for both days or for day 1 only.
Please note, there will be a limit of 80 spaces for day 2

If you have a disability, specific access requirements or any special dietary requirements we need to be made aware of please contact the organisers using the details above.

We look forward to welcoming you to Birmingham in March 2019

Prof. Davide Calebiro
Dr Steve Thomas
Dr Dee Kavanagh
Dr Jeremy Pike
Dr Natalie Poulter
Sharmaine Afferion

The organising committee would like to thank our industry partners for their generous support.


 Workshop Sponsors

In Partnership: The Universities of Birmingham and Nottingham

University of Birmingham
B15 2TT

Telephone: +44 (0)121 414 3974

The University of Nottingham
University Park,

Telephone: +44 (0)115 846 7554