TS6 Szeged 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 17th (all candidates informed of the final selection)
  • Confirmation & payment before Dec 14th

Aim & topics:

If your research requires use of image processing and analysis, or you are responsible for support and training of researchers and need a more solid understanding of DIP techniques and building of workflows, then this school is for you.
Consequently, for this ECI school we expect basic experience with one toolbox such as ImageJ/FIJI, MatLab or similar. Scripting/coding skills are NOT necessary. 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: macros/scripting of workflows
  • Extracting and validating quantitative numerical data from bioimages
  • Sessions to work on own problem, code your workflow and explore different tools with help from experts

If you are an absolute beginner without images or experience we recommend waiting for the next edition in the fall of 2018 (Edinburgh UK).
If you are interested mostly in automation and scripting of worlflows we reccomend the “staff” school in the fall of 2018 (Edinburgh UK).
If you are experienced with DIP & analysis, have already trained other users and/or are actively involved in building and designing workflows, we suggest applying to TS7 for “Analysts” (same venue and dates). The next Analyst school will  take place in Luxembourg early 2019.

More info & testimonials about previous editions here and 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 basic experience with a tool like ImageJ or similar (not recommended for absolute beginners who have never used an IA tool)
  • 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 (value is explained in application form) well in advance of school dates and by bank transfer only!
  • Must comply to administrative conditions and confirm travel+hotel one month in advance (please read conditions at end of the application form).


Schedule/programme (final)

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

Jan27 , Sat
“Process & automate”

  • 9:00 Late arrivals & Welcome
  • 10:00 Intro; building workflows & macros
  • 15:00 2D segmentation & particle analysis
  • DIP techniques, feature enhancement, morphomats
  • 21:00 “Natural history of fake data” lecture

Jan28, Sun
“Analysis workflows”

  • 9:00 3D Object analysis with 3D OC + Suite
  • Cell/particle tracking with TrackMate
  • 15:00 FishQuant exercise, pt1
  • Icy: data visualization & visual programming
  • 21:00 Webtool Lecture

Jan29, Mon
“outside the toolbox…”

  • 9:00 MatLab intro
  • 11:30 FishQuant pt2 (in Matlab)
  • 13:30 social event all afternoon!
  • 18:00 Catch-up or work on own data

Jan30, Tue
“…& wrap-up”

  • 9:00 Machine learning with CellProfiler Analyst
  • 3D Visualization with BigDataViewer and Drishti
  • 15:00 work on own data, present results & wrap up
  • free evening (no dinner!)

Jan31- Feb2

(3 days)

All TS6 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, exercises, and instructions/solutions)
  • Trainees receive a free pass to the Symposium 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 not included for trainees
  • NEW! Free shuttle service Budapest -> Szeged and return after Schools or Symposium
  • There is a limited number of travel grants available (see below), but grants are paid ONLY after the school

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 (https://www.inf.u-szeged.hu/kutatas/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; 1.5€) for two stops to the TS venue (from Széchenyi tér to Aradi vértanúk tere). Hotel prices are really cheap and there is also the possibility of sharing rooms if you need to save on your stay (please ask TS6 organizers).

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 closed!