!NEW TS12 Porto 2019

6th Training School for Early Career Investigators (TS12), Porto  2019

  • Porto, October 14-17 (Mon-Thu), 2019 
  • Number of available seats for trainees:  25
  • Invited trainers: >10
  • Application deadline: TBA
  • Results from selection: TBA
  • Administrative fees must be processed by July 15th!


  • (NOTE – this school in NOT introductory, and is opened for both researchers and imaging facility staff, who need to get more in depth training on building and automation of IA workflows. If you are an imaging facility staff member whose work focuses on providing support to users, and you feel already confortable with basic IA workflows and now need training focused on scripting with ImageJ/FIJI and python, we reccommend TS13 in the same venue)
  • Principles, techniques and ethics of digital image processing (DIP); publication of bioimages.
  • Building practical workflows to analyse 2D, 3D & time-lapse bioimages (eg. object segmentation and densitometry, spot detection & tracking or filament tracing)
  • Introduction to workflow automation: record & reuse commands, scripting of workflows/pipelines
    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.
  • Must comply to administrative conditions and confirm travel & hotel by deadline (see above) – read conditions at end of application form!

Trainers (more being confirmed!)

  • Fabrice Cordelières – Bioimage Analyst & Microscopy Specialist @CNRS/Bordeaux Imaging Center, France
  • Kota Miura – Bioimage Analyst @University of Heidelberg, Germany & NIBB, Okazaki Japan
  • Robert Haase Bioimage Analyst @MPI-CBG, Germany
  • ...

Brief programme (under construction!)

Programme organizers: TBA
morning coffee-breaks @10:30/16:30, lunch @12:30, dinners @19:30

Day 1
Process & automate”

  • 9:00 Welcome
  • Intro (ImageJ), interface. tricks, tools & utils; help and document workflows.
  • Programming for ImageJ, recorder, loops, statements etc...
  • “Natural history of fake data” lecture
Day 2
Analysis workflows

  • Tracking objects in IJ + BigData manipulation;
  • Filters and morphomats; Segmentation & ML
  • Webtool : BISE & Biasflow
Day 3

  • TBA
  • TBA
  • Work on own data
  • 18:00 Gala dinner
Day 4

  • Work on own data, discuss code, present results & wrap up

What is, and what is not, included?

  • Students needs to bing their own laptops to follow the school and exercises.
  • Once accepted we will contact you with instructions to install all materials
  • All trainees are provided with coffee breaks, lunch and dinners and 1 gala dinner
  • Travel & accommodation are not included for trainees (see below how to travel to venue and hotels nearby).

Venue & contacts

Local Organizers

Paula Sampaio (sampaio(at)ibmc.up.pt)
i3S – Instituto de Investigação e Inovação em Saúde
Universidade do Porto
Rua Alfredo Allen, 208; 4200-135 Porto, Portugal
Site: http://www.i3s.up.pt
Google map link: https://goo.gl/maps/yvstCwa8Wmp
Joao Paulo Cunha (INESCTEC)
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
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 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.

i3S is a trans-disciplinary Health Sciences 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.

The institutes are each other at 15 min walking distance

{info about Porto }


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)

A number of hotel rooms have been pre-booked for the NEUBIAS Training Schools and Taggathon. When making your reservation, please be sure to specify your participation in the NEUBIAS event to benefit from the negotiated room rate. {PROMO CODE AND DEADLINE?}.

{instructions to go from hotels to venue}

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 provide less than 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 (daily signature on attendance sheets compulsory for grantees). The grants are attributed at a fixed rate (check registration form for more info) to cover for travel and accommodation.

 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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