PPBI
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
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:
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- 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:
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- May 5th – morning - a walk through of the Amira program - this will be fairly generic to give everyone an overview of this program
- May 5th – afternoon - a more dedicated tutorial on preselected data based on the needs of the participants (LM or EM? 2D or 3D? etc)
- May 6th - morning - a continuation of the dedicated tutorial
- May 6th - afternoon - the chance to work with your own data with help from the Amira specialists in the room
- May 7th 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
9 - 12 December 2019 | IGC - Lisbon
Modern biology poses complex problems that can only be technically addressed by multidisciplinary approaches and a high level of specialisation. This is the genesis of core facilities and scientific services, accelerators for research by providing some technical abstraction and standardising applications.
In order to learn what these facilities do and to raise awareness about the available resources, the Instituto Gulbenkian de Ciência (IGC) is organising the 3rd edition of biomethods. This workshop aims to give to PhD students, early postdocs, and technicians a general overview of the current technical approaches in modern biology, including hands-on in the labs.
The registration is free but mandatory. The workshop is limited to 40 participants and selected based on motivation.
For detailed program, registration, and other information please visit the workshop website http://biomethods.site/
The workshop will take place at the IGC in the Protagoras auditorium, on the library building.
The organising committee
Nuno Moreno and Manuel Rebelo
Batch analysis and macro development in ImageJ/Fiji: going beyond the basics | 2nd edition
9, 10, 11, 14 and 15 December 2020 | ONLINE COURSE
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 will focus on how to automate routine tasks (for conditions where many images need to be processed), as well as how to deal with more complex image analysis situations, to 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. At the course, this 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.
Previous knowledge on the basics of bioimage analysis is recommended, but no prior experience in ImageJ macro development is required or assumed, nor any prior programming skills.
CONTENTS
- Introduction to batch analysis: from macro recorder to simple scripts.
- ImageJ macro language syntax.
- From GUI (graphical user interface) workflows to scripts: exploring ImageJ’s built-in functions and developing user-defined functions.
- Automatic data loading: access-list of files in a given directory and filter it by text patterns in file name or by extension.
- Batch processing from scripts.
- Combine multi-dimensional information: programmatically identifying image pairs (e.g. multichannel, time-lapse) and combine information.
- From Image data to tables: extract information to tables and personalize output variables on output tables (data logging).
- Export sample images and customized tables to a directory.
More information and registration: https://www.i3s.up.pt/training?v=118
Introduction to data analysis and image processing with MATLAB - 5th Ed. @ i3S
25-27 March 2019 | i3S, Porto
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.
Lecturer: Paulo de Castro Aguiar, i3S / INEB
TA: Ana Filipa Gerós, i3S / INEB
Prerequisites: None – previous experience with MATLAB is not required
Participants are asked to bring their laptops (a MATLAB trial version is available)
Early Bird | Until 3rd February 2019
i3S members - 130 € | Payment deadline: 13th February 2019
External participants - 150 € | Payment deadline: 13th February 2019
Late registration | 4th February until 3rd March 2019
i3S members or External participants - 200 € | Payment deadline: 13th March 2019
(registrations accepted up to a maximum of 20 participants)
Course on Optical Microscopy Imaging for Bioscience - 11th Edition @ i3S
01-05 April 2019 | i3S, Porto
The 11th edition of the Optical Microscopy Imaging for Bioscience 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 and will include theoretical and hands-on practical sessions. Specialists in microscopy will teach the lectures and the major microscopy companies support the practical sessions.
Target Audience:
The course is designed to master and PhD students, early career researchers plus all other researchers interested in acquire skills in optical microscopy.
Registration:
Early Bird | Until March 3rd 2019
i3S members - 200€
External Participants - 270€
Payment deadline: March 10th 2019
Late registration | March 4th until March 17rd 2019
i3S members - 250€
External Participants - 325€
Payment deadline: March 24th 2019
For more information and registration: https://www.i3s.up.pt/content/training?v=72
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