TS5 Gothenburg 2017

2nd Training School for Facility Staff (TS5), Gothenburg 2017

  • Gothenburg- September 11-14th (Mon-Thu), 2017 
  • Number of available seats for trainees:  25
  • Number of available trainers to assist: >10


  • ImageJ macro language, 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
  • Image analysis workflows with actual biological problems (based also on expressed interests of selected applicants). The official course textbook is “Bioimage Data Analysis”, a freely downloadable textbook. The training will include some of those exercises as well as new topics.

Who should apply? Staff scientists, graduate students, post-docs or faculty who work in the context of Bioimaging facilities and provide assistance and training to users in need of Bioimage Data Analysis.

More info & testimonials about previous edition here…


  • We expect experience in handling image data and familiarity with imageJ/FIJI; this course is not appropriate for complete beginners (NEUBIAS is offering also a Training School for Early Career Researchers)! Very basic programming knowledge is a plus, but not a requirement.
  • Although not required, it is advisable to bring own data & workflow proposal.
  • Must fill valid application form by June 2nd – follow link at end of this page.
  • Applicants are required to write a letter of motivation (pasted into registration form), mention their current level of proficiency and interests, propose a workflow and dataset(s) to test & improve, and show significant potential for knowledge dissemination.
  • Must be able to attend all days/times of the course (no exceptions!).
  • Must be able to pay administrative charges by bank-transfer (credit card or paypal payment not possible).
  • Must comply to administrative conditions (as explained in the end of application form) and, after being selected, send confirmation of travel arrangements before the end of July.


  • Fabrice Cordelières – BioImage Analyst & Microscopy Specialist @ CNRS/Bordeaux Imaging Center, France
  • Giovanni Cardone  – BioImage Analyst @ MPI Biochemistry, Germany
  • Hendrik Deschout, Bioimage Analyst @ Gothenburg University, Sweden
  • Ignacio Arganda-Carreras –  Developer @ Dep. Computer Science & Artificial Intelligence, Basque Country Univ, Donostia-San Sebastian, Spain
  • Jan Eglinger – Image Processing Specialist @ Friedrich Miescher Institute, Switzerland
  • Joakim Lindblad – Researcher & Analyst @Centre for Image Analysis, Uppsala Univ, Sweden
  • Kota Miura – Image Analyst @University of Heidelberg, Germany & NIBB, Okazaki Japan
  • Mitko Kostov – Researcher & Analyst @St. Kliment Ohridski University, Faculty of Technical Sciences, Bitola, Macedonia
  • Moritz Kirschmannn, Researcher @Center for Microscopy and Image Analysis, Univ. of Zurich
  • Ofra Golani BioImage Analyst @Weizmann Institute Rehovot – Israel
  • Paula Sampaio –  Facility manager at  @ I3S/IBMC. Porto, Portugal
  • Peter Horvath – PI & Developer @Biological Research Centre of the Hungarian Academy of Sciences
  • Sébastien Tosi – Image Analysis specialist@IRB – Barcelona, Spain
  • Stefan Helfrich Bioimage Analyst @ Bioimaging Center, University of Konstanz, Germany
  • Stephan Preibisch – PI &Developer @Berlin Institute for Medical Systems Biology (BIMSB), Germany
  • Volker Baecker – Bioimage Analyst and Software Developer @ INSERM, France

Brief programme (final)

morning coffee-breaks @10:30, lunch @12:30, afternoon breaks @16:00 and dinners at ~19:30

Day 1 (Sept 11, mon)

  • 8:00!!! Welcome session @Wallenberg Center
    (TS5 will then transfer to computer-room at the Sahlgrenska Academy, starting at 9:00 every morning)
  • 9:00 Introduction to IJ macro language
  • Batch IJ macro
  • Segmentation
  • Welcome reception dinner

Day 2 (Sept 12, tue)

  • 9:00 Segmentation (cont…)
  • Advanced scripting
  • Seminar: “Lightsheet Image Reconstruction and the Application to Whole Organism Transcription Imaging” 
  • Tracking & Track
  • Stitching
  • Buffer dinner

Day 3 (Sept 13, wed)

  • 9:00 Intro to MATLAB
  • Matlab and Image processing
  • 2D & 3D visualization
  • 2D worflow
  • Discussion of advanced workflows
  • 8:00 Gala dinner!

Day 4 (Sept 14, thu)

  •  9:00 Intro to KNIME
  • Present your problem, model your workflow, work on own data
  • Show your results
  • 18:00 School finishes!

What is, and what is not, included?

  • All participants (including the 25 selected trainees) are provided with catering of coffee break, lunch and dinner (excluding breakfast) and course material in electronic format.
  • 1 workstation available for each trainee with all materials pre-installed. If you prefer to bring your own laptop please choose the right selection in the application form (if accepted we will contact you with instructions to install all materials; keep in mind that MatLab licenses may be available only in the local workstations!). *UPDATE – trainees will not be allowed to connect their laptops to the room’s ethernet, so only the room’s workstations will be used for training.
  • Travel & accommodation are not included for trainees (see below how to travel to venue and hotels nearby).

Venue & contacts

The 2017 NEUBIAS Workshop 2 will be hosted by the Centre for Cellular Imaging, Sahlgrenska Academy, at the University of Gothenburg, Sweden.

The Sahlgrenska Academy is the faculty of health sciences at the University of Gothenburg. Education and research are conducted within the fields of pharmacy, medicine, odontology and health care sciences. The  Wallenberg Conference Centre is a modern meeting center located next to the Sahlgrenska Academy at Medicinaregatan 20. The Sahlgrenska area is reached by car, bus or tram (the closest stop is ‘Medicinaregatan‘)

2017Gothenburg.AkademiskaHus(Foto: Akademiska hus)

Travel & Hotel info:

Getting to Gothenburg

By air: Göteborg Landvetter Airport is an international airport serving the Gothenburg region in Sweden. It is located 20 km south-east of the city centre and you can travel directly from various destinations in Europe and the world. For general information, please click here.

  • Airport transfer

It’s easy to get to and from the airport with the shuttle bus service Flygbussarna and the journey time is between 25 and 30 minutes. Buses leave from right outside the terminal building and the final stop is the main bus station Nils Ericssonterminalen in central Gothenburg. Taxi or rental cars are also available at the airport.


By train: SJ, Tågab and NSB are running frequent services to and from the Central Station in Gothenburg, connecting the city with the Scandinavian capitals Stockholm, Oslo and Copenhagen. The journey times are just under 4 hours from Oslo, around 3 hours from Stockholm and 3,5 hours from Copenhagen. The trains from Denmark stop at Copenhagen international airport, making it a convenient option to fly there and catch the train to Gothenburg.

By bus: The bus terminal Nils Ericsson terminalen is serviced by long distance and express bus companies like Swebus and Nettbus. You can easily travel to Gothenburg from the major cities in Sweden and Scandinavia.

By car: The main Training venue is at the Conference Centre Wallenberg, Medicinaregatan 20A in Gothenburg. The largest parking area is located between the tram stop ‘Medicinaregatan’ and the conference center (6 SEK/h). A smaller parking lot is available on the right side of the conference centre, next to the small cottages (15 SEK/h). There is also a parking garage at Medicinaregatan 16. Parking directly in front of the Wallenberg center is not allowed for visitors.

Getting around in Gothenburg

Local buses and trams are run by Västtrafik.

Venue: The main Training venue is at the Conference Centre Wallenberg, Medicinaregatan 20A. The closest tram stop is called Medicinaregatan. The Gothenburg city public transportation system can be found here.

  • From the Göteborg Landvetter airport to the Venue

Take the airport bus, Flygbussarna, in front of the arrivals terminal. The bus runs every 15-20 minutes, and it is only 20 minutes ride to the city centre. You can find the time tables and how to buy tickets here.

Get off at Korsvägen stop and take tram number 6 with direction ‘Länsmansgården via Sahlgrenska’, tram number 8 with direction ‘Frölunda’ or tram 13 with direction ‘Sahlgrenska’. Get off at Medicinaregatan stop.

  • From Nils Ericsson terminal (bus terminal) to the Venue: Take a tram number 6, 7 or 13 from the bus terminal, Nils Ericsson terminal, to Medicinaregatan stop.
  • From city centre to the Venue: Tram number 7 and 8 also stop there if coming from other directions.2017Gothenburg.Simon_paulin-gothia_towers-3986(Foto: Gothia towers at Korsvägen. Photographer Simon Paulin/imagebank.sweden.se)

Staying in Gothenburg

Hostels: A hostel is a good alternative if you are traveling on a tight budget. These two hostels are located close to the meeting venue: Slottsskogen Hostel and Linnéhostel

Hotels: The University of Gothenburg has agreements with these following hotels and as a participant in the Training Schools and Taggathon you can get a discounted price. See each hotel below for the terms. However, it is advisable to make a reservation as soon as possible since rooms fill up fast. Other hotels can be found at e.g. the go:teborg webpage.

Quality hotel Panorama (3 stars) Single room 882 SEK/night (~92€, VAT included). To get access to the group discount send email to Reservation.q.panorama@choice.se with your personal info, dates of arrival+leave, and mention booking code 2028GR007045.

Hotel Lorensberg (3 stars) Single room 897 SEK/night (~93€, VAT included). State the booking code JM225 to get the discounted prices.

Hotel Vasa (3 stars). Single room 795 SEK/night (~83€) and double room (one 140 cm wide bed) 910 SEK/night (~96€). State “Neubias” to get the discounted price.

Inform them that you attend Training School or Taggathon arranged by the University of Gothenburg and that you are entitled to our discounted prices.

Local Organization (&contacts)

The Sahlgrenska Academy is home of the  Centre for Cellular Imaging (CCI), lead by Julia Fernandez-Rodriguez, the local organizers of the NEUBIAS event.
The CCI, in operation since 2003, is one of a number of advanced technology platforms at the University of Gothenburg. This multimodal advanced microscopy facility provides technical and scientific excellence by the integration of multiple imaging technologies in a single core. Our vision is that the CCI will allow users to think broadly and select the best possible instrument(s), light and/or electron microscope(s), to provide detailed answers to their scientific questions at the highest resolution. We are committed to developing a functional systems microscopy approach, which can address new scientific questions with a multi-modal imaging strategy using only a few or many samples. Using modern cell biological tools, expertise in live cell imaging and state-of-the-art equipment and image analysis we will continue to help researchers relate structure to function and morphology to mechanism.

Local Organizers

  • Julia Fernandez-Rodriguez (e-mail), Maria Smedh (e-mail), Hendrik Deschout (e-mail), Carolina Tägemo
  • Ai-Linh Nguyen (email), Carina Johansson (admin)

Staff Training School programme:

The local organizers wish you a wonderful stay in Gothenburg!

(Foto: Klippan Gothenbrurg. Photographer: Per Pixel Petersson/imagebank.sweden.se

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 before June 30th, and grants will be executed after the Training School (daily signature on attendance sheets compulsory for grant winners). The grants are attributed at a fixed rate of 750€ to cover for travel and accommodation.

 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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