Batch analysis and macro development in ImageJ/Fiji: going beyond the basics | 3^rd Edition  

24-26 November 2021 | i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto

This course is designed for ImageJ/Fiji users who want to go beyond the basics and progress to more intermediate/advanced analysis with this software.

The course focuses on how to automate routine tasks (for conditions in which many images need to be processed), as well as how to deal with more complex image analysis situations and maximize information extraction.

Although ImageJ can be used with its graphical user interface, the implementation of a workflow to multiple images requires the development of macros and/or scripts for batch processing.

In this course, the process is tackled by building up from the development of very simple macros to more complex workflows, where images are processed and information acquired in an automated or semi-automated way.

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Biomolecular interaction analysis 2021: From molecules to cells 

25-29 October 2021 | Virtual 

A comprehensive and integrated characterization of molecular interactions is key to the understanding of life processes at a molecular level. Due to their complexity the study of binding events requires the gathering of data from multiple methods in order to build a complete picture of their function.

This EMBO Practical Course aims at a multidisciplinary approach to the study of molecular interactions from and in biological systems, integrating biochemical/biophysical methodologies with live cell microscopy techniques.

In this 5^th edition, this EMBO Practical Course will cover a range of methods used in the kinetics and thermodynamics characterization of binding events, such as:

Isothermal Titration Calorimetry (ITC),

Surface Plasmon Resonance (SPR),

Electrically Switchable nanolevers (switchSENSE), and

Microscale Thermophoresis (MST)

The bridge to in vivo will be crossed with the introduction of advanced light microscopy techniques, e.g.:

Fluorescence Resonance Energy Transfer (FRET) and

Fluorescence Lifetime Imaging (FLIM),

to study the dynamic interactions of proteins within the living cell.

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Introduction to digital bioimage analysis | 3^rd Edition

11-15 October 2021 | Online

Due to the SARS-CoV-2/COVID-19 pandemic situation, it might happen that an on-site course cannot take place. In that case, an online version of the course will be organized from 11th to 15th (afternoons) October with the same program. 

With the advent of the digital era, nowadays images are multidimensional numerical data that can be processed and analyzed quantitatively to extract more information. With this course, we intend to give a general introduction to ImageJ/Fiji (imagej.net/), show how to use it to extract quantitative data, and how to write simple macros.

CONTENTS

-    Principles, techniques and ethics of digital bioimage processing.
-    Basic commands of ImageJ/Fiji software.
-    Working with multidimensional (2D, 3D, time-lapse, position) bioimages.
-    Enhancement and processing of images.
-    Extract quantitative numerical data.
-    Design of simple workflows for automation of image analysis with ImageJ macros.
-    Advanced ImageJ plugins (stitching, registration, colocalization)

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BioImage Analysis for High Content Screening 

25-28 May 2021 | ONLINE

High Content Screening generates a massive amount of image-based data in the biosciences field. Images contain diverse and valuable quantifiable data, however, many researchers lack the knowledge to extract those data in a practical, fast and repetitive way. Fundamentally practical, in this modular course, participants will get acquainted with several open-source image analysis software (ImageJ/Fiji, ilastik, CellProfiler, CellProfiler Analyst, Cytoscape and IDEAS®) designed to deal with large amounts of images. Experimental data will be used as datasets for image segmentation and quantification.
This course is organized in modules. Therefore, participants are free to choose the image analysis tools more convenient to their own work.

Tissue Clearing Online Workshop

18-20 May 2021 | ONLINE

Tissue clearing is a technique that enables visualization of opaque organs and tissues in 3-dimensions (3-D) by turning tissue transparent. The major challenge that underlies most of the unsuccessful applications of tissue clearing is that every application requires its own protocol and optimization approach.

This 3 days online workshop will cover various topics in tissue clearing, from protocol optimization, light-sheet microscopy imaging to 3D visualization and quantification. This is an opportunity for participants to learn and discuss tissue clearing protocols and applications and to contact with state-of-the-art light microscopy systems for imaging of the cleared tissue samples, guided by an experienced staff. Participants will also explore processing and image analysis workflows to extract the best information from the data.