NEW! TS6 Szeged, Feb 2018

Training School TS6 for Early Career Investigators

  • Jan 27-30th (Sat-Tue), 2018
    • Selected trainees are invited to attend Symposium for free (requires separate registration!)
  • Number of available seats for trainees:  25
  • Number of available trainers to assist them >10
  • Registration deadline: Nov 9th!
  • Selection results: Nov 11th
  • Confirmation & payment before Dec 14th

Aim & topics:

If your research requires use of image processing and analysis, or if you are responsible for support and training of researchers and need a better understanding of techniques, then this school is for you!
Consequently, for this edition, we expect some previous experience on basic image processing using one toolbox such as ImageJ/FIJI, MatLab, Icy, CellProfiler or others.
The school will address:

  • The principles, techniques and ethics of digital image processing (DIP)
  • Building of practical workflows to analyse 2D, 3D & time-lapse bioimages
  • Different toolboxes
  • Workflow automation: scripting of workflows/pipelines
  • Extracting and validating quantitative numerical data from bioimages.
  • Sessions to solve your problem, code your workflow and explore different tools with help from Analyst

If you are an absolute beginner without images or experience we recommend waiting for the next edition in the fall of 2018.
If you are experienced with DIP & analysis, have already trained other users on image analysis and/or are actively involved in building and designing workflows, we suggest applying to TS7 for “Analysts” (same venue and dates).

More info & testimonials about a previous edition here…


  • Applicants must have own data and preliminary results, bring them to the school, and explain why and what they need to learn about image analysis to advance their research (explained in application form)
  • Must have experience with a tool like ImageJ or similar and be prepare to explain in the registration form your experience and demonstrate status and level of experience.
  • Must fill valid application form before November 9th – follow link at the end of this page
  • Must explain their motivation by mentioning level of proficiency and interests, and propose a mini-project with goals for the school (e.g., a specific image analysis tool or workflow they are interested in getting help from our expert trainers)
  • Must be able to attend all days and times (no exceptions!)
  • Must guarantee payment of administrative fees well in advance of school dates and by bank transfer only!
  • Must comply to administrative conditions and confirm travel and hotel at least one month in advance– please read the conditions at end of the application form!

Trainers (confirmed, more to be invited)

  • Abel Szkalisity – Image Analyst @Biological Research Center of the Hungarian Academy of Sciences, Szeged Hungary
  • Fabrice Cordelières – Image Analyst & Microscopy Specialist @CNRS/Bordeaux Imaging Center, France
  • Giovanni Cardone  BioImage Analyst @ MPI Biochemistry Martinsried, Germany
  • Jean-Yves Tinevez, BioImage Analyst @ Pasteur Institute – Paris, France
  • Kota Miura – Image Analyst @University of Heidelberg, Germany & NIBB, Okazaki Japan
  • Paulo Aguiar – PI & BioImage Analyst @ INEB/i3S,  Porto Portugal
  • Peter Horvath – PI & Developer @Biological Research Centre of the Hungarian Academy of Sciences, Szeged Hungary
  • Ofra Golani BioImage Analyst @ Weizmann Institute Rehovot, Israel
  • Sébastien Tosi BioImage Analyst @ ADM IRB Barcelona Spain
  • Simon Noerrelykke  BioImage Analyst @ ETH Zurich, Switzerland

Schedule/programme (preliminary)

(Morning coffee breaks @10:30, lunch at @13:30, afternoon breaks @17:00 and dinners at ~20:00)

Jan27 (Saturday)

  • 9:00-10:30 Welcome
  • 10:30 Intro; building effective workflows
  • 15:00 DIP techniques
  • 17:30 ImageJ macro language – catch up
  • 21:30 Work on own project (not confirmed!)

Jan28 (Sunday)

  • 9:30 Plenary lecture
  • 10:30 CellProfiler & Analyst
  • 15:00 Segmentation  (TBA)
  • 17:30 Cell Tracking (TrackMate)
  • 21:30 Work on own project (not confirmed!)

Jan29 (Monday)

  • 9:30 Plenary lecture
  • 10:30 MatLab & ImageJ
  • 13:30 Lunch + social event
  • 18:30 Multi-toolbox workflow
  • 21:30 Work on own project or Tagging activity

Jan30 (Tuesday)

  • 9:30 Plenary lecture
  • 10:30 3D visualization
  • 15:00  Work on own data
  • 17:30 Present & Wrap up
  • 20:00 Dinner & free evening

Jan31- Feb2

(3 days)

All TS participants invited!

Program here:

What is, and what is not included for trainees?

  • Upon selection of 25 trainees, all participants are provided with catering (coffee break, lunch and dinner, excluding breakfast) and all course materials in electronic format (including lectures and exercises).
  • Each trainee will have a free pass to the symposium starting after the schools, with access to all sessions and events.
  • Room is equipped with workstations, one per trainee, so it is not necessary to bring your own laptop.
  • Travel and accommodation are not included for trainees
  • There is a limited number of travel grants available (see below!).

Venue & contacts

TS6 will take place at the Institute of informatics of the University of Szeged.


University of Szeged, Institute of Informatics

The Institute of Informatics was established in 1990 as part of the Faculty of Science and Informatics at the University of Szeged. Its main task is to teach modern computer science and information technology and to take part in innovative and research-and-development projects. The Institute offers BSc, MSc and teacher training programs and also provides basic education of informatics at several other programs of the Faculty of Science and Informatics at the University of Szeged.

Students have the chance to travel, work or do research abroad, to study one or two semesters at foreign universities, and are also welcome to join the research projects going on at the Institute.

MSc graduates interested in research can join one of the many exciting research projects of our PhD School of Informatics, established in 2002.

Besides performing educational tasks, the Institute implements research-and-development and innovative projects with institutional and industrial partners.

The Institute publishes an English language journal, Acta Cybernetica (, which is an important forum and output of research activity and PhD training.

Hotels & Local Transport

For participants of TS6 rooms have been pre-booked in Hotels Tisza and Art (more information on the Symposium page). Both hotels are reasonably priced and close to the venue. When students learn about the selection results (Nov 15th), they should contact the hotel of choice directly, mention code “NEUBIAS2018” and confirm reservation dates and billing information (check page above for details about payment process and deadlines).

Hotel Tisza and Hotel Art are both within walking distance (10 minutes and 4 minutes) from the Training Schools’ venue. From Hotel Tisza you can also take the tram (line 1 or 2) for two stops to the TS venue (from Széchenyi tér to Aradi vértanúk tere).

Travel Grants

NEUBIAS will offer competitive travel grants to a number of trainee applicants affiliated to institutions in COST member countries or Near-Neighbor Countries or approved European RTD Organizations (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 November 16th, and grants will be executed ONLY after the training school (daily signature on attendance sheets compulsory for grant winners). The grants are attributed at a fixed rate of 650€ to cover for travel and accommodation expenses.

Selection Criteria (for all, including granted trainees):

Trainees will be selected based on their scientific motivations. Upon selection, NEUBIAS will seek proof of the candidates status as “Early Career Investigator” (COST defines ECI as a researcher whose career spans up to eight years after the PhD/doctorate) and of being actively working on the project described in the application form. 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. Evaluation 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? Applications are now open here…