TS13 Porto 2019

4th Training School for Facility Staff (TS13), Porto  2019

  • Porto, October 14-17 (Mon-Thu), 2019 
  • Number of available seats for trainees:  25
  • Invited trainers: >10
  • Application deadline: May 30
  • Results from selection: 2nd week of June (changed!)
  • Confirmation and processing of admin fees by July 15


  • This school  is opened for imaging facility staff members whose work focuses on supporting users, and who feel already confortable with basic IA workflows and now need training focused on scripting with ImageJ/FIJI and Python
  • Principles, techniques and ethics of digital image processing (DIP); publication of bioimages.
  • Extracting and validating quantitative numerical data from bioimages
  • "WOYOD" - solve your own problem, code your workflow and explore different IA strategies with help from Analysts

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  • MUST BE ABLE TO BRING OWN LAPTOP and prepare it in advance!

  • Must have own data to bring to the school which they have started analysing, and be able to explain what they need to learn about image analysis to advance their research (explained in application form).

  • Must already have experience with a toolbox such as ImageJ/FIJI.
  • Must submit valid application form (link at the end of this page) before the deadline (see above) - no exceptions!
  • Must include brief letter of motivation (text pasted into registration form), mentioning level of proficiency and interests, and propose a mini-project with goals for the school (e.g., a specific image analysis workflow or tool - what help is required from our expert trainers?)
  • Must be able to attend all days/times of the course (no exceptions!)
  • Must be able to bank-transfer administrative charges (see below).
  • Must comply to administrative conditions and confirm travel & hotel by deadline (see above) – read conditions at end of application form!


  • Anna Klemm – Staff Scientist @Center for Image Analysis / SciLifeLab, Uppsala, Sweden
  • Arianne Bercowsky Rama - Analyst @EPFL, Switzerland (former Analyst School trainee)
  • Jan Eglinger – Image Processing Specialist @ Friedrich Miescher Institute, Switzerland
  • Jean-Yves Tinevez - Bioimage Analyst & Developer @Pasteur Institute – Paris, France
  • Kota Miura – Bioimage Analyst @University of Heidelberg, Germany & NIBB, Okazaki Japan
  • Mafalda Sousa - Bioimage Analyst @i3s, Univ Porto (former Analyst School trainee)
  • Marion Louveaux - Researcher, Analyst @Ruprecht-Karls-Universität Heidelberg, German
  • Robert Haase - Bioimage Analyst @MPI-CBG, Germany (former Analyst School trainee)
  • Uwe Schmidt - Developer @@MPI-CBG, Germany

Brief programme

Coffee-breaks @10:30/16:30, lunches @12:30

Day 1 "Scripting with FIJI"

  • 9:30 Welcome & intros @iNESCTEC
  • Advanced ImageJ programming
  • git intro
  • CLIJ
  • Work on own data
  • “Natural history of fake data” lecture @I3S

    (Free night)

Day 2 "Scripting with FIJI"

  • Tracking 
  • ImageJ/ImgLib2 API
  • Macine Learning
  • Work on own data
  • Webtool : BISE & Biasflow

    (Free night)

Day 3
“Scripting with Python”

  • Python scikit-image
  • Python; data analysis; plotting
  • Lecture
  • PyImageJ
  • Work on own data

    18:00 Gala dinner

Day 4

  • Big Data Handling
  • Work on own data
  • Student presentations and farewell

    School ends at 16:00

Fees, conditions and what is, and what is not, included ?

  • Attendance to all days of the course is mandatory for all accepted trainees
  • Participants need to bring their own laptops to follow the school and exercises.

  • Once accepted we will contact trainees with instructions to install all materials

  • Accepted trainees will be asked to pay administrative fees (350 euros, except if affiliated to ITC* countries: 200 euros)

  • Trainees receiving a travel grant from COST (see below) do not pay any fee.

  • All trainees are provided with coffee breaks, lunch and 1 network dinner

  • Travel & accommodation arrangements are not included for trainees (see below how to travel to venue and hotels nearby).

    *: ITC countries Inclusiveness Target Countries: Albania, Bosnia and Herzegovina, Bulgaria, Cyprus, Czech Republic, Estonia, Croatia, Hungary, Lithuania, Latvia, Luxembourg, Malta, Moldova, Montenegro, Poland, Portugal, Romania, Slovenia, Slovakia, Republic of North Macedonia, Republic of Serbia and Turkey.


Venue & contacts

Local Organizers:

Paula Sampaio (IBMC/i3S)
Joao Paulo Cunha (INESC TEC)


Programme organizers:

Arianne Bercowsky Rama - (EPFL, Switzerland)

Jan Eglinger – (Friedrich Miescher Institute, Switzerland)

Robert Haase (MPI-CBG, Germany)

Enquiries should be addressed to: neubias.ts@gmail.com



The TS12 will be hosted at two leader research institutions of Porto: INESC TEC and i3S

INESC TEC - Institute for Systems and Computer Engineering, Technology and Science is a research institution, dedicated to scientific research and technological development, technology transfer, advanced consulting and training, and pre-incubation of new technology-based companies. The 13 R&D Centres of INESC TEC are structured in four thematic domains - Computer Science, Industry and Innovation, Networked Intelligent Systems, and Power and Energy, which hosts over 700 integrated researchers. 

Address: Campus da Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
Site: https://www.inesctec.pt
Google map link: https://goo.gl/maps/WXtgTcSpmRD2

i3S – Instituto de Investigação e Inovação em Saúde is a trans-disciplinary Health Sciences research institution whose mission lies on the promotion of science and technology development, while creating an environment that feeds real breakthrough research and translation of discoveries into the clinic research. i3S focuses on three Integrative Programs: Cancer, Host Response and Interaction, and Neurobiology and Neurologic Disease, encompassing 68 research groups and over 1000 researchers.

Address: Rua Alfredo Allen, 208; 4200-135 Porto, Portugal
Site: http://www.i3s.up.pt
Google map link: https://goo.gl/maps/yvstCwa8Wmp

The institutes are each other at 15 min walking distance

About Porto

Porto is Portugal’s second largest city and the capital of the Northern region.
Located along the Douro river estuary in northern Portugal, Porto is one of the oldest European centres. Its settlement dates back many centuries when it was an outpost of the Roman Empire. Its Latin name, Portus Cale, has been referred to as the origin for the name “Portugal”.

Porto’s Historical Centre was registered as a World Heritage Site by UNESCO in 1996. The city is traditional and historical, but also contemporary, which can be seen in its streets, its monuments and its museums.

Icons such as “Serralves” or “Casa da Música” and a regular agenda of music, art and sports events stand witness to urban space, in constant movement.

One of Portugal’s internationally famous exports is the port wine, produced exclusively in the Douro region and aged in cellars.

Porto Convention Visitors Bureau on Vimeo.

Visit Porto & the North
Porto Guide
10 Reasons Why Porto is the Best Place for a Winter Break


Travel & Hotel info:

How to get to Portugal/Porto

From the airport to the city center:

The closest airport to Porto city is Francisco Sá Carneiro Airport. The airport is well connected to the city center offering the following options:

  • Shuttle Service: Direct connection between the Airport and the City| Connection average time: 20 minutes | Ticket price: 6 € | More information: http://100rumos.com
  • Metro: Line E – “purple” | Destination Station: Trindade | Connection average time: 25 minutes | Ticket price: 1,80 €| More information: http://www.metrodoporto.pt
  • Bus: Bus number 601 | Destination Station: Cordoaria | Connection average time: 30 minutes | Ticket price: 1,80 € | More information: http://www.stcp.pt/en/travel
  • Taxi | Connection average time: 15 minutes | Average price: 25 € extra-chargers for luggage and night hours may be charged.

From Porto city center to i3S and INESC TEC:

The easiest way to reach the venues is by metro:

  • Line D – yellow (direct line) | Destination Station: Hospital São João; leave at station: Pólo Universitário (i3S) or IPO (INESC TEC)  | Average time: 10 minutes | Single travel ticket price: 1,20 € | More information: http://www.metrodoporto.pt/en/
  • i3S is at exit of  Pólo Universitário station
  • To reach INESC TEC exit at the IPO station and go straight on following the Rua do Dr. Plácido da Costa (Dr. Plácido da Costa Street). At the end of this road, cross over onto the Rua do Dr. Roberto Frias and the Faculty of Engineering from the University of Porto will be in front of you.
  • From other Metro lines to Line D - yellow change at station: Trindade

The venues can be also reached by Bus. More information: https://www.stcp.pt/en/travel/

Staying in Porto (suggested hotels)

Hotels at walking distance to venues:


Hotels in city center:


Along the yellow Metro line you can find several other hotels and airbnb options.

The local organizers welcome you to Porto!


Travel Grants

NEUBIAS will offer competitive Travel Grants to a number of the Trainees applicants affiliated to institutions in COST member countries or Near-Neighbour Countries or approved European RTD Organisations (check definitions in COST Vademecum here). Please check in the application form how to apply for those grants by filling the additional fields enabling to submit a justification. We typically support about 1/3 of the grant applications received, so any documented information provided to demonstrate why you need a travel grant is important for us to fully assess your request. The grants are supported by COST (funding body of the NEUBIAS Action). Eligibility and reimbursement modalities will follow the criteria/general COST policies (check the Vademecum here). Granted trainees will be notified before June 30th. Please be aware that grants can only be executed AFTER the Training School (and upon daily signature on attendance sheets mandatory for grantees). The grants are fixed amount (check registration form for more info) meant to support travel and accommodation expenses of granted trainees.


Selection Criteria (for all, including granted Trainees):

Trainees will be selected on the basis of their scientific motivations, as described in their motivation letter. Upon selection, NEUBIAS will seek proof of the candidates status as "early career investigator" or "staff" and of being actively working on the project(s) as described in the motivation letter. Gender balance and geographical distribution will be taken into consideration according to COST policies, and only after pre-selection of eligible/suitable candidates and in the case that applicants are too numerous as compared to the number of available seats. Evaluations of the applications is operated by "double anonymous" (no mention to name, institution, country) review by the Training Schools Evaluation Committee of NEUBIAS.

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