Training School for Early Career Investigators: Oeiras 2017

  • Oeiras - Feb. 12 (Sun) - 15th (Wed), 2017 
  • Number of available seats for trainees:  25
  • Number of available trainers to assist them: 6-10
  • Deadline for applications: December, 2nd 2016
  • Selection results communicated 2nd week of December

Topics addressed:

  • Principles, techniques and ethics of digital image processing
  • Enhancement & processing of bioimages for analysis and publication
  • Building practical workflows with free GUI tools (ImageJ/FIJI, Icy and CellProfiler) to analyse 2D, 3D & time-lapse bioimages
  • Introduction to workflow automation (record and reuse commands/pipelines)
  • Extracting and validating quantitative numerical data from bioimages
  • Solve your own IA problem, create your workflows, explore different tools!

Selected Testimonials

"I had a great time. The course was extremely useful and interesting. It covered loads of different concepts and common questions/ problems in image analysis. We were learning immensely while having fun. The general atmosphere was very informal and relaxed, with great food, drinks and with plenty of moments to socialize and meet both students and trainers."

" It was a great opportunity to consult results from our own data with experts in the field."

"It was an AMAZING course, and it exceeded my expectations."

"...excellent and I thought it was very much what early career scientists need"



Alexandre Dufour - PI & Developer. @ Institut Pasteur.  Paris, France

Carolina Wahlby - PI & Image Analyst @ Uppsala Univ, Sweden

Chong Zhang – BioImage Analyst @ Univ Pompeu Fabra. Barcelona, Spain

Christian Tischer -  BioImage Analyst @ EMBL. Heidelberg, Germany

Daniel Sage - Developer @ EPFL. Lausanne,  Switzerland

Daniel White - Bioimage Analyst @ G&E Healthcare

Fabrice Cordelières – BioImage Analyst @ CNRS/Bordeaux Imaging Center. Bordeaux, France

Hugo Botelho - Bioimage Analyst @ FCUL, Lisbon, Portugal

Nuno Martins (previous NEUBIAS Trainee!) - Microscopy specialist @ IGC, Lisbon, Portugal

Paulo Aguiar – PI & BioImage Analyst @ INEB/i3S.  Porto, Portugal

Paula Sampaio –  Facility manager at  @ I3S/IBMC. Porto, Portugal

Perrine Paul-Gilloteaux - Bioimage Analyst @ Univ de Nantes, France


Day 1 “Using IJ for Scientific Illustration”

  • Introduction to ImageJ: basic operations
  • Checking and preserving the quantitative intensity content of your images
  • Working with color images and images in color
  • From pixels to microns: ROIs, image calibrations and simple measurements
  • Working with stacks: 3D image visualisation
  • Assembling data for publication using FigureJ

Day 2 “Using IJ for Image Analysis, building workflows”

  • Working with pixels: filters, morphomaths and binary operations
  • Working with objects: measurements in 2D and 3D
  • Microscopy Image Restoration: DeconvolutionLab2
  • Recording simple macros for batch processing: example 1
  • From workflows to simple batch macros: example 2

Day 3 "“Building Image Processing Workflows with CellProfiler & Icy”

  • Building a workflow with CellProfiler
  • Building a workflow with Icy
  • Ethics in Digital Image Processing

Day 4 “Choose your toolbox, Work on your data and Present your results”


The 2017  NEUBIAS2020 training schools (ECI & Analysts) were hosted by the Instituto Gulbenkian de Ciencia in Oeiras (Portugal) ->Fact&figures about the IGC<-

The IGC is a research institute devoted to biological & biomedical research and graduate training. Excellence, originality, communication, cooperation and generosity, coupled with an outstanding infrastructure are the ingredients that make IGC a special place. Established (and still supported) by the Calouste Gulbenkian Foundation in 1961, the IGC was profoundly restructured in 1998 to form the institute that runs nowadays. Small independent research groups work in an environment designed to encourage interactions and exploit synergies, with minimal hierarchical structure. The scientific programme of the IGC is multidisciplinary, including Cell and Developmental Biology, Evolutionary Biology, Immunology, Host-Pathogen Interactions, Disease Genetics, Plant Biology, Neurosciences, Theoretical and Computational Biology. The IGC is home of the “UIC:Advanced Imaging Unit”, lead by NEUBIAS2020 Local organizer Gaby G Martins.


Local Organization:

  • Gaby Martins: gaby [at] igc.gulbenkian.p and Pedro Fernandes pfern (at), Nuno P Martins (IGC), Hugo Pereira (IGC)
  • Anna Fejfer: amfejfer [at] + Pedro Alves: ppalves [at] (admin team)

ECI Training School programme:

  • Fabrice Cordelières: fabrice.cordelieres [at]
  • Paulo Aguiar: pauloaguiar [at]
  • Christian Tischer:  tischer [at]


igc_logo1   logo_fundacao_60anos_pt1



How to get there? (click here to get google maps directions from your current location!)

Upon arriving at the Lisbon international airport there are 3 options to get to Oeiras (IGC & INATEL) or Carcavelos (Riviera or Praia-Mar hotels):

1- Airport shuttle ( line#1 "City Center" and exit at the last stop in "Cais-do-Sodre"; from there take train headed to Cascais, exit in "Oeiras" for IGC or INATEL, or continue to "Carcavelos" for the Riviera or Praia-Mar hotels (see interactive map below).

2- Subway metro: first take RED line from the Airport to "Alameda" station, then switch to GREEN line headed to "Cais-do-Sodre", and from there take train headed to Oeiras/Carcavelos. Click here for a google map with directions of this route!

3- A Taxi ride com Airport to Oeiras is ~24km and should cost ~30€. A taxi ride do "Cais do Sodre" + train to Oeiras/Carcavelos is another option. Keep in mind that this option is not eligible to COST refund!

Interactive map of Oeiras/Carcavelos POIs & Venue:


Hotels near the IGC (Training school & taggathon venue):

INATEL (1.3km from IGC, 1km from Oeiras train station); breakfast included, wifi only on common areas!)
telf: +351 210 029 800
- "Superior" rooms 40€ per single, 45€ double - >20 such rooms available.
- "Standard" rooms 35€ single, 40€ double ~15 rooms available
- "Tourist" rooms (no A/C!, and not renovated!), 28€ single, 35€ double ~20 rooms available
(mention NEUBIAS2020 in email to get special price, but don't try to use it if reserving online!)

Student dorm at EstacaoAgro (~500m from IGC, 1km from Oeiras train station; NO breakfast; student dorm, not Hotel!)
telf: +351 962926027 (contact is Ms Umbelina)
- "Single" rooms (with private WC), 21.4€ - 11 rooms available

Riviera Hotel in Carcavelos (3km from IGC, 500m from Carcavelos train station; breakfast and wifi included)
telf: +351 21 458 6600
- "single" room 70€ (mention NEUBIAS2020 in email but don't try to use it online!) >10 rooms available (unconfirmed)

Praia Mar Hotel in Carcavelos (3km from IGC, 700m from Carcavelos Station; breakfast and wifi included)
Telf: +351 21 458 5100
- "single" room ~60€ (mention NEUBIAS2020 in email but don't try to use it online!) >10 rooms available (unconfirmed)

Other possibilities to search in Air B&B, Booking or Trivago:
- search locations near "Rua Quinta Grande, Oeiras", the IGC is near the "Jardim do Palacio do Marques do Pombal" and "Camara Municipal"