free amp templates

WORKSHOPS

Community and Industry workshops info

Mobirise

Community

Several sessions which address key topics from image processing to advanced imaging, prepared and presented by your peers

Mobirise

Industry @ room

Series of presentations on technical advances and applications directly from manufacturers, will occur in a dedicated room

Mobirise

Industry @ booth

Series of presentations on technical advances and applications directly from manufacturers, will occur directly at the manufacturer's booth

Community Workshops

Speakers:

soon

Session Description:

soon

Speakers:

soon

Session Description:

soon

Speakers:

» Pedro Matos Pereira (@P_Matos_Pereira)

» Siân Culley (@SuperResoluSian)


Session Description:

Despite the widespread use of Super-Resolution techniques, most methods remain technically challenging and involve sophisticated hardware and/or software tools. In 2014, Expansion Microscopy (ExM) was introduced as an alternative to overcome this challenge. The concept is extremely simple: instead of super-resolving your target of interest you physically expand your sample in such a way that the structure is now above the diffraction limit (the expansion is 4 to 5 fold the original size) and image it on a conventional microscope. The original method served to deliver super-resolution information to researchers without access to a super-resolution system. However, ExM versatility was limited by technical details like the need for special labelling probes. Several improvements were made since then to enhance its applicability, such as introducing changes that made ExM compatible with conventional probes, like commercially available labelled antibodies and endogenous fluorescent proteins. Additionally, ExM can also be combined with classical super-resolution microscopy techniques effectively allowing to combine the resolution increase from both approaches. ExM has been applied to a variety of samples, from eukaryotic cells and tissues to pathogens such as bacteria or virus, making it an excellent alternative to classical super-resolution approaches.

Speakers:

» Sébastien Tosi
» Ignacio Arganda Carreras

Session Description:

Deep learning, the latest extension of machine learning, has pushed the accuracy of algorithms to unseen limits, especially for perceptual problems such as the ones tackled by computer vision and image analysis. This workshop will cover the foundations of the field, the communities organized around it, and some important tools and resources to get started with these techniques. Some successful applications of deep learning, especially in the field of bioimage analysis, will be presented and some hands-on will cover how to setup a working deep learning environment. No prior programming knowledge is required to follow the workshop.

Speakers:

» Julien Colombelli
» Gabriel Martins 

Session Description:

Mesoscopy is a new generic term that comprises the techniques allowing 3D fluorescence imaging of very large samples in toto (mm to centimeters). Mesoscopy has seen a fast pace of development recently due to improvements in light-sheet microscopy, optical tomography, and tissue clearing techniques. Because of the small offer of commercial systems to do mesoscopy, several labs have, in the past 5-6 years, begun developing DIY and even open source solutions for implementing these techniques, for example the openSPIM, OpenSpin microscopy, OPenT, MesoSPIM, LegoLISH or OptiSPIM.

In this small workshop we will demonstrate the principles of light sheet and optical tomography, some of the subsystems necessary to assemble a working mesoscope and a brief demo of how 3D mesoscopic datasets are acquired. 

Speakers:

» Erin Tranfield
» Mafalda Silva
» Ana Laura Sousa 

Session Description:

Correlative Light and Electron Microscopy: Introduction to experimental
procedures, as well as tricks and tips for successful experiment planning and execution.
 
Session Program: 

1. Intro to the different kinds of CLEM and some of the challenges of CLEM
2. CLEM applications: how to answer biological questions 
3. Discussion about how to start a project and when CLEM is an appropriate
4. Demonstration of CLEM tools

Speakers:


» Siân Culley (@SuperResoluSian)

» Pedro Matos Pereira (@P_Matos_Pereira)

Session Description:

In this session, we will look at Fiji workflows for single molecule localization microscopy (SMLM) data. The main points that we will cover are:

1. Analysis of sparse blinking datasets: the ‘classic’ SMLM dataset
• Use of QuickPALM and ThunderSTORM to localize individual molecules
• Interpretation of particle tables
• Drift correction
• Rendering and visualisation of images

2. 3D SMLM data sets
• Different types of 3D calibration data
• Localization and visualisation in ThunderSTORM

3. Dense blinking datasets: the ‘tricky’ SMLM dataset
• Use of HAWK for pre-processing dense data
• Options in ThunderSTORM for fitting dense data
• Using SRRF for live-cell data

4. Multicolour datasets
• Chromatic aberration correction using NanoJ

5. Assessing data quality
• Using SQUIRREL to measure the resolution of images and to assess the quality of images.

Homework: To prepare for this session, participants are asked to install Fiji (https://imagej.net/Fiji/Downloads). We will be using the following plugins:
• QuickPALM (pre-packaged into Fiji)
• ThunderSTORM (installation instructions at: https://github.com/zitmen/thunderstorm)
• HAWK (https://www.coxphysics.com/ - copy the version 1.1 .jar file into the plugins folder in your Fiji install)
• NanoJ-Core, NanoJ-SRRF, NanoJ-SQUIRREL (In Fiji, go to Help>Update…>Manage Update Sites and check the boxes for NanoJ-Core, NanoJ-SQUIRREL and NanoJ-SRRF. Close this window, then press ‘Apply changes’

We will also be using various test data sets (which we will provide or the participants can bring their own) 

Speakers:

» María Victoria Gomez

Session Description:

soon

Industry Workshops @ room

Industry Workshops @ booth

© Copyright 2019 SPAOM - All Rights Reserved