PPBI

Portuguese Platform of BioImaging

PPBI - Portuguese Platform of BioImaging

National Research Infrastructure for Open-access to Bioimaging resources

Member of Portuguese Roadmap for Research Infrastructures of Strategic Interest

PPBI Euro-BioImaging Node

Introduction to digital bioimage analysis, 2^nd Edition

September 23-25 and 28-30, 2020 | ONLINE COURSE

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. This edition will be online (ZOOM) sessions with a practical approach.

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.

More information and registration: https://www.i3s.up.pt/training?v=119

Matlab

Introduction to data analysis and image processing with MATLAB - 6^th Edition

04-07 May 2020 | ONLINE COURSE

Quantification is an essential component in every scientific domain, and the ability to extract more information from the data is a fundamental asset. This is an introductory "hands-on" course where the concepts and techniques will be explored directly in the MATLAB environment. MATLAB is a well-established tool in scientific and technical computing, with key advantages such as being extremely versatile/powerful and easy to learn. This course is especially suited for people engaged in research wanting to start using MATLAB in the context of scientific data analysis and image processing (quantification). Participants are invited to bring their own data and an analysis problem of interest to be addressed in the course (as a project), with the help of the tutors.

- Previous experience with MATLAB is not required

PREREQUISITES

- Participants are asked to bring their laptops (a MATLAB trial version is available)

PROGRAM

Introduction to computer algorithms.
The MATLAB environment.
Variables and basic array operations.
Strategies for representing numerical/scientific problems in a computer.
Plotting data.
MATLAB programming.
Creating functions and scripts.
Automating data analysis.
Image analysis: images as arrays of data values; importing images and metadata; operations on image data; filtering; segmentation; morphological operations; properties measurements

More information and registration: https://www.i3s.up.pt/training?v=102

Course on Optical Microscopy Imaging for Biosciences | 12^th Edition (Canceled)

23-27 March 2020 | i3S, Porto

The 12^th edition of the Course on Optical Microscopy Imaging for Biosciences offers to the participants a comprehensive light microscopy course that explores the fundamentals of light microscopy and introduces the state-of-art of advanced fluorescence microscopy techniques. The course will flow from sample preparation to quantitative image analysis. It will include theoretical lectures taught by specialists in the field and hand-on practical modules supported by the major microscopy companies where the participants will have the opportunity to take work with high-end microscopy resources.

Program Topics
Specimen preparation;
Light proprieties and image formation;
Optical contrast techniques in transmission light microscopy;
Fluorescence microscopy techniques: wild-field, laser scanning confocal, two-photon, TIRF and light-sheet; Live cell imaging;
Analyzing biomolecular interactions and dynamics: FRET, FLIM, FRAP, PA, FC;
Super-resolution microscopy;
Quantitative image analysis.

REGISTRATION

Early Bird | Until February 7^th, 2020
i3S members and PPBI nodes staff - 200€
External Participants - 270€
Payment deadline: February 13^th, 2020

Late registration | From February 8th to February 29^th, 2020
i3S members - 250€
External Participants - 325€
Payment deadline: March 5^th, 2020

More information and registration: https://www.i3s.up.pt/training?v=116

NEUBIAS Training Schools 14 &15 @ Bordeaux

February 29 - March 3, 2020 | Bordeaux, France

Applications for Training Schools TS14 and TS5 are now open!!!

NEUBIAS, the Network of European BioImage Analysts (www.neubias.org), is delighted to announce two new Training Schools on BioImage Analysis:

TS14 for Early Career Investigators (Life Scientists: PhD candidates, Postdocs, Staff, ...): This training school will cover the basics of image analysis using ImageJ/Fiji, as well as image analysis workflow automation using ImageJ macro programming. In addition, it will be taught how to use the software package ilastik for machine learning based image segmentation and object classification, and how to integrate ilastik into ImageJ macro based workflows. Moreover, an overview of further relevant bioimage analysis software packages will be given and there will be ample time for "Work on Your Own Data" sessions assisted by experienced Analysts.

TS15 for BioImage Analysts (advanced level): This school targets bioimage analysts, who are willing to enhance their professional scope and techniques for improving the quality of their analysis, as well as willing to contribute with their knowledge and experience to the school. Prerequisite is a proficiency in at least one programming language (we do not train coding). The school focuses on workflow designing. This year, we will have a particular emphasis on statistics for bioimage analysis and related tools e.g. R and Python libraries. In addition, we will overview machine & deep learning components.

The schools will be held in Bordeaux, Feb 29 - Mar 03 2020, hosted at the Centre Broca Nouvelle-Aquitaine by the Bordeaux Imaging Center (BIC) and the Interdisciplinary Institute for Neuroscience. The selected students will be able to attend the whole NEUBIAS conference as part of the training.

NEUBIAS schools are an excellent opportunity to learn from many experts in Bioimage Analysis (we are expecting >20 specialists at the event) and “…a great mix of intensive learning and community networking” (former trainee testimonial). All schools include practical sessions “Work on Your Own Data”, plenary seminars and a session on ethics in image analysis.

Applications are now open (TS14 = 25 seats, TS15 = 35 seats and ~10 trainers per school). Within the COST framework (funders of NEUBIAS), we will offer up to 7 travel grants per school to applicants who qualify.

Application deadline: December 12th 2019

Selection notification: December 20th 2019

More information about schools (programme & trainers) and venue, travel & lodge available at our website:

eubias.org/NEUBIAS/training-schools/

eubias.org/NEUBIAS/training-schools/eci/ts14-bordeaux-2020/

eubias.org/NEUBIAS/training-schools/analysts/ts15-bordeaux-2020/

Amira Practical Course

May 5-6, 2020 | IGC

Thermo Fisher Scientific, the Portuguese Microscopy Society (SPMicros) and the Portuguese Platform of BioImaging (PPBI) are pleased to announce an Amira Practical Course. The course will be kindly hosted by the Instituto Gulbenkian de Ciência and it is open to Scientists based within Portugal.

The main objective of this course is to give the Portuguese research community a better understanding of the Amira software and enrich the applications of this tool in 2D and 3D data analysis for light and electron microscopy images.

In an effort to achieve that main objective, before the course each participant will:

- receive a trial license;
- receive a list of tasks to try with the program;
- need to practice some of the basic skills.

This advance "homework" is meant to maximize the learning opportunities in the Amira Practical Course and it is highly advised that interested course participants reserve time in their schedule for this work prior to the start of the course.

Draft Program:

- May 5^th – morning - a walk through of the Amira program - this will be fairly generic to give everyone an overview of this program
- May 5^th – afternoon - a more dedicated tutorial on preselected data based on the needs of the participants (LM or EM? 2D or 3D? etc)
- May 6^th - morning - a continuation of the dedicated tutorial
- May 6^th - afternoon - the chance to work with your own data with help from the Amira specialists in the room
- May 7^th onwards - Homework to analyse the data with full support from the technical experts of Amira for the duration of the 1 month trial license.

We only have 20 spots in the computer room and we have a small charge to cover the costs of lunch and the logistics of hosting this course.

Thank-you to ThermoFisher for sponsorship and the Portuguese Microscopy Society (SPMicros) and the Portuguese Platform of BioImaging (PPBI) for co-organization of this Practical Course.

More information: http://facilities.igc.gulbenkian.pt/electronmicroscopy/electronmicroscopy-amira.php

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PPBI

PPBI

PPBI - Portuguese Platform of BioImaging

PPBI Euro-BioImaging Node

PPBI Courses (4)

External Courses (0)

Training Archive (47)

NEUBIAS Training Schools 14 &15 @ Bordeaux

Draft Program: