NEUBIAS Training School for Facility Staffs: Barcelona,  Sept 13 – 16, 2016

Topics addressed:

  • BioImage analysis and programming foundations
    • ImageJ macro language; Macro recorder, editor & macro language; variables & strings;user-defined functions; loops & conditional execution; batch processing and automation
    • Filtering, segmentation, post-processing & measurement
    • Matlab basics; import, processing and basic analysis; Matlab programming
  • Applications
    • Cell nuclei segmentation
    • 3D Colocalization analysis
    • 3D tubular network analysis of blood vessels
    • Directionality analysis of EB1 movement along microtubules
    • 3D data visualization and registration
  • “Present you problem… code your workflow”!

The official course textbook is “Bioimage Data Analysis”, a freely downloadable textbook where more details about most of these topics can be found. Trainees are encouraged to bring it either printed or accessible in a tablet/e-book reader.

Programme & Schedule

Coffee breaks are served daily ~11:00 and 16:00, lunches at 13:00 [1.5h] and dinners at 21:30!

Day 1 (Sep 13th, Tue)

  • 9:00 Registration and welcome
  • 10:00 Intro to IA and workflows
  • 11:30 Introduction to ImageJ macro language
  • 17:00 Batch iJ macro process
  • 20:30 Neubias project

Day 2 (Sep 14th, Wed)

  • 9:00 Q&A
  • 9:30 3D Colocalization analysis
  • 14:30 3D Blood vessels
  • 18:30 Meet the taggers 1 (casual): opportunity to meet analysts working to build new NEUBIAS resources (see Taggathon)
  • 19:45.21:00 free time [NEUBIAS members meeting]

Day 3 (Sept 15th, Thu)

  • 9:00 Q&A
  • 9:30 Introduction to Matlab
  • 11:30 2D Image processing and data analysis with Matlab
  • 14:303D visualization with Matlab
  • 15:30 3D Image processing and workflows
  • 18:30 EB1 tracking exercise
  • 20:00 Meet the taggers 2 (play & tag)

Day 4 (Sept 16th, Fri)

  • 9:00 Q&A
  • 9:30 EB1 trakcing (cont)
  • 14:30 Open session: Present your problem, code your workflow, get help from trainers
  • 18:00 course ends!

Trainers TS#1


Trainer Position Where
Benjamin Pavie BioImage Analyst @ VIB Leuven, Belgium
Fabrice Cordelières BioImage Analyst @ University of Bordeaux Bordeaux, France
Gaby Martins Microscopy @ Gulbenkian Institute of Science Lisbon, Portugal
Giovanni Cardone BioImage Analyst @ MPI Biochemistry Martinsried, Germany
Joakim Lindblad BioImage Analyst at Mathematical Institute of the Serbian Academy of Sciences and Arts Belgrade, Serbia
Kota Miura BioImage Analyst at EMBL Heidelberg – Germany
Ofra Golani BioImage Analyst @ Weizmann Institute Rehovot – Israel
Paulo Aguiar Principal investigator @ INEB / I3S Porto – Portugal
Petter Ranefall BioImage Analyst at Center for Image Analysis Uppsala – Sweden
Romain Guiet BioImage Analyst at BIOP / EPFL Lausanne – Switzerland
Invited Local Trainers (Barcelona)
Anna Bosch Microscopy @ CCiTUB Univ. of Barcelona
Chong Zhang BioImage Analyst @ UPF Univ. Pompeu Fabra
Sébastien Tosi BioImage Analyst @ ADM IRB Barcelona
Manel Bosch Microscopy @ CCiTUB Univ. of Barcelona
Julien Colombelli Microscopy @ ADM IRB Barcelona


Barcelona Venue & Contact


The first NeuBIAS Workshop will take place at the Poblenou Campus of Universitat Pompeu Fabra in Barcelona, where the Department of Information and Communication Technologies (DTIC) is located.


Tallers Area
Campus Poblenou, Universitat Pompeu Fabra
Roc Boronat 138
08018 Barcelona
Catalonia, Spain

Local transportation

Poblenou Campus is easily accessible both by public transport: Metro (L1 Glòries, L4 Llacuna),  Tram (T4 Ca l’Aranyó, T5 i T6 La Farinera), Train (Clot-Aragó), and Bus (H14, B25, B20, 192, 92, 42, 40, 7, 6). It is also easily accessible by  private transport but parking slots are really reduced.


Contact information

Local contact: Chong Zhang (chong.zhang(at)upf(dot)edu)
phone: +34 935422163

Travel and accomodation

Please arrange your travel by yourself!

Here are our recommendations upon their availability (Please refer to “NEUBIAS UPF WORKSHOP” in your booking email!):

IBIS GLORIAS 99 Ciutat de Granada, 99 Tel: 34 93 300 7777

UPF price (before 28th July, 2016): 75 € (if stay between Sep 11th and Sep 17th)


Diagonal , 205 08018 Barcelona Phone: +34 93 489 53 00 Email:

UPF price (before 28th July, 2016): 99 € (Single), 114 € (double) (booking code: NEUBIAS nº 1258729if stay between Sep 13th and Sep 17th)


Av.Diagonal,161-163 08018 Barcelona Phone: 34 93 486 88 00 / Fax: +34 93 309 67 27 e-mail:

UPF price (before 28th July, 2016): 104 € (Single), 114 € (double) (if stay between Sep 11th and Sep 17th)

Google maps indicating hotel locations

If you have problems with booking (before 28th July) of any of these hotels listed above, please contact Joana (joana.clotet(at)upf(dot)edu).

Further inquiries / Contact

Please contact Gabriel Martins and Fabrice Cordelières for information related to the Training School organization and content:



Kindly sponsored by: 


Applications were closed on July 15th 2016!

Who should apply?

Staff scientists, graduate students, post-docs and faculty, who work in the context of Bioimaging facilities and provide assistance to users in need of Bioimage Data Analysis. We expect some experience in handling image data, and a good level of familiarity with imageJ/FIJI; this course is not appropriate for complete beginners! (in 2017 NEUBIAS will offer more NEUBIAS Training Schools including one for “Early Career Investigators”) Very basic programming knowledge is a plus, but not a requirement.

Interested applicants should prepare a letter of motivation (max 2000 char.!), provide contact information and fill a form to assess their level of proficiency and interests; applicants are also encouraged to provide details about a mini-project that they wish to bring to the course (e.g. a specific image analysis tool or workflow that they are interested in getting help with, from our expert trainers).

  • Number of Available Seats for Trainees:  25
  • Number of available Trainers to assist them: 11

If you are an early career investigator and have no experience with image processing or analysis, NEUBIAS will organize the first training school for Early Career Investigators (at the Gulbenkian Institute, Portugal, 12-15 Feb 2017) dedicated to Life Scientists that aim at diving into BioImage Analysis.

If you already master BioImage Analysis tools and feel you have a solid understanding of workflows and programming, NEUBIAS will also organize an advanced course for Analysts, focused on developing advanced workflows and applications, and delivered by developers and confirmed analysts (at Gulbenkian Institute, Oeiras – Portugal, 12-15 February 2017).


  • Must be able to attend all days/times of the course (no exceptions!)
  • Must fill valid application form by July 15th (2016).
  • Must comply to administrative conditions and send confirmation of travel arrangements BEFORE JULY 31st (2016) after confirmation of selection on July 18th (2016)

Travel Grants

NEUBIAS will offer competitive Travel Grants to a number of the Trainees applicants, affiliated to institutions in COST member countries, Near-Neighbour Countries or approved European RTD Organisations (check definitions in 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 July 18th, 2016, and grants will be executed after the Training School (daily signature on attendance sheets compulsory for grant winners).

The grant amounts to about 920 euros in concept of travel and accommodation for this 4-days (i.e. 5 nights) Training School, to be reimbursed upon acceptance and after participation, according to COST rules (check the Vademecum here).

What is Included

COST supports Local organizers with a financial contribution and supports Trainers. Lunch and coffee breaks will be included for all participants. The course material will be delivered electronically and on pen-drives.

Complementary expenses, not covered by eligible expenses supported by COST, will be incurred to the participants. Check the application form for more details.

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. 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.