!NEW TS9 Edinburgh 2018

3rd Training School for Facility Staff (TS8), Edinburgh 2018

  • Edinburgh October 16-19 (Tue-Fri), 2018 
  • Number of available seats for trainees:  20
  • Number of available trainers to assist: >10
  • Application deadline: TBA
  • Selection of candidates: TBA


  • 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 editions 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.


  • TBA


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

Day 1

  • 8:30 Welcome
  • 9:00 Introduction to IJ macro language
  • Batch IJ macro
  • Segmentation

Day 2 

  • 9:00 Segmentation (cont…)
  • Advanced scripting
  • Seminar: “TBA” 
  • Tracking & Track
  • Stitching

Day 3

  • 9:00 Intro to MATLAB
  • Matlab and Image processing
  • Seminar: “TBA” 
  • 2D & 3D visualization
  • 2D worflow
  • Discussion of advanced workflows

Day 4

  •  9:00 Intro to KNIME
  • Seminar: “TBA” 
  • 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

TS8 and 9 will be hosted by the MRC Centre for Regenerative Medicine and its Imaging facillity (http://www.crm.ed.ac.uk/facilities/imaging).
The venue will be at:
SCRM Building
The University of Edinburgh
Edinburgh bioQuarter
5 Little France Drive
EH16 4UU

Travel & Hotel info:

Getting to Edinburgh…

Staying in Gothenburg


Local Organization (&contacts)

Local Organizers

Staff Training School programme:

  • TBAThe local organizers wish you a wonderful stay in Gothenburg!


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 (application form will be available soon)?