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


  • Principles, techniques and ethics of digital image processing
  • Enhancement & processing of bioimages for analysis and publication
  • Building practical workflows with free GUI tools to analyse 2D, 3D & time-lapse bioimages
    (using trainees' own images requiring eg. object segmentation and densitometry, spot detection & tracking or filament/tube tracing)
  • Introduction to workflow automation (record and reuse commands/pipelines)
    • NOTE - the focus of the ECI TS is on workflows with GUI tools, so it is not the ideal course for researchers who are already advanced into image analysis or are interested mostly in learning scripting or ij macro language! NeuBIAS will organize other Training Schools with that emphasis.
  • Extracting and validating quantitative numerical data from bioimages/data mining
  • Solve your own IA problem, create your workflows, explore different tools!


  • No specific level in image analysis knowledge is required, HOWEVER applicants should have own data to bring to the course and a well explained critical need for image analysis to advance their research work (to be presented in application form).
  • Must fill valid application form by November 30th (2016) - follow link at end of this page
  • Applicants are required to write a letter of motivation (paste into registration form), mention their current level of proficiency and interests, and propose a mini-project with goals for the course (e.g., a specific image analysis tool or workflow that they are interested in getting help with from our expert trainers)
  • Must be able to attend all days/times of the course (no exceptions!)
  • Must comply to administrative conditions and send confirmation of travel arrangements BEFORE December 16th (2016) after confirmation of selection (December 6th 2016) - make sure to read conditions at end of application form

Trainers (confirmed)

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

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

Juergen Reymann -  Bioimage Analyst @ ZBSA, University of Freiburg, Germany.

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.

Schedule (provisional)

Every day at 11:00 a quick coffee break is served in room to minimize interruptions; at 16:30 a full coffee break is served and there is an opportunity for TS2, TS3 and Taggathon participants to interact.

Sun 12th

9:00 - Welcome

9:30  “The components and how they work”

  • Intro to ImageJ and digital images; where to find help, commands and install plugins
  • Multidimensional bioimages (3/4D & composite, RGB vs Lab); image metadata & image properties
  • Intensity profiles and basic image statistics; use of ROIs and measuring signal vs noise vs background in fluorescence images

12:30 Lunch

13:30 resume

  • Projection of stacks; orthogonal & arbitrary slices and 3D viewer (rendering)
  • Surface (topology) plots, kymographs
  • Preparation for publication eg using ImageJ & FigureJ and exporting a movie

16:30 Coffee Break

17:00 3h block 

19:00 Dinner at Restaurant in Oeiras

Mon 13th

9:00 Q&A

9:30 "IP part of workflows"

  • Contrast enhancement; Image filters & noise removal; Background/illumination correction; color correction & enhancement in iJ
  • The analysis workflows: Image segmentation, edge detection, feature extraction, binarized images & masks; Binary operations (morphological maths) in imageJ
  • Recording & saving commands in ImageJ and saving as macro; apply to all images in a folder
  • talks/discussions
    • Discussion on ethics of digital image processing + Quantification of  fluorescence? eg, “bad data, now what?”
    • DeconvolutionLab 2 - microscopy image restoration

12:30 Lunch

13:30 Building a workflow in IJ and record as Macro: Practical workflow 1 (particle detection + expression/fluorescence co-localisation) results output

16:30 Coffee Break

17:00 Practical workflow 2: Tracking with TrackMate or Cell tracking in tissue packing: Time-lapse - filter + watershed + erode + 3DObjectsCounter + measure cell area across time

20:00 Dinner @ Restaurant in Oeiras

Tue 14th

9:00 Q&A

9:30 Building a workflow in CellProfiler: Building a pipeline for detecting tissue culture cells and quantification of fluorescence in organelles in each cell + 15min Demo of HTM explorer for data inspection

12:30 Lunch

13:30 Building a workflow in Icy: quick overview and features that make icy more intuitive or productive than ImageJ (and how to find them); contrast “graphical programming” with ij scripting

16:30 Coffee Break

17:00 Building a workflow with Knime: from images to numbers

20:00 Dinner @ Restaurant in Cascais

Wed 15th

9:00 - Welcome

9:30 Choose your toolbox, code your workflow, analyse your images and present results

13:00 Lunch

14:00 Departure to Symposium in Lisbon (all TS trainees get free passes for the symposium!)

What is, and what is not, included?

  • Upon selection (25 trainees), all participants are provided with catering (coffee break, lunch and dinner, excluding breakfast) and course material in electronic format and on pen-drives.
  • Participation to the NEUBIAS Symposium (15-17th of February, right after the Training School) is included for all training school participants - sessions + coffee breaks + lunches; bus Transfer to the Symposium on Feb 15 is also included.
  • Gala dinner at the Symposium will be offered for applicants who submit an abstract before November 30th!
  • Travel and Accommodation are not included (see below how to travel to the IGC and hotels nearby).
    • However, there are 3 grants available - check form for more information.
  • Check the application form for more details (link below).

Venue & contacts (both training schools and Taggathon)

The 2017  NEUBIAS2020 training schools (ECI & Analysts) will be hosted by the Instituto Gulbenkian de Ciencia in Oeiras (Portugal)

Address: R. Quinta Grande, 6 1780-156 Oeiras – Portugal    ->Fact&figures about the IGC<-


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"


After you've secured a room in Oeiras for 12-15th Feb, please don't forget you need a room close to the Symposium in Lisbon (15-17th Feb), commuting from Oeiras to the Symposium venue can take as long as 1h (walk+train+walk+subway!) so its not ideal!

Looking forward to receiving you all in Oeiras!

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.

Contact information

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]

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. 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 by December 20th and grants will be executed after the Training School (daily signature on attendance sheets compulsory for grant winners). The grant amounts to ~900€ for travel and accommodation, to be reimbursed against real expenses and upon acceptance, and after participation, according to COST rules (check the Vademecum here).

 Selection Criteria (for all, including granted Trainees):

Trainees will be selected strictly 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" 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.


Ready to apply (click to access application form)?


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