TS9 Edinburgh 2018

3rd Training School for Facility Staff (TS9), Edinburgh 2018

  • Edinburgh October 16-19 (Tue-Fri), 2018 
  • Number of available seats for trainees:  20
  • Invited trainers: >10
  • Application deadline: May15th
  • Results from selection: May 30th
  • Confirmations and travel grants: To be announced!
  • Payments must be processed before July 15th!


  • ImageJ macro language, recorder & editor; macro language; variables, strings, user-defined functions, loops & conditional execution; batch processing and automation.
  • Filtering, segmentation, post-processing & measurement + tracking
  • Matlab basics; import, processing and basic analysis; Matlab programming
    Interfacing between Matlab and Omero.
  • 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 dedicated mostly or exclusively to bioimaging facilities and providing direct assistance and training to users. Should have potential for dissemination.


  • 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 in the same venue/dates)! Basic programming knowledge is a plus, but not a requirement.
  • Accepted trainers will be sent a brief tutorial to prepare in advance for the school!
  • Although not required, it is advisable to bring own data & workflow proposal to discuss with trainers and test during school
  • Must fill valid application form (link at the end of this page) BEFORE the deadline (see above)
  • Applicants are required to write a small 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 potential for dissemination.
  • Must be able to attend all days/times of the course (no exceptions!)
  • Must be able to prove status as “facility staff” and obtain institutional support letters
  • Must be able to pay administrative charges by bank-transfer (credit card or paypal payment not possible) before July 15th 2018.
  • Must comply to administrative conditions (as explained in the end of application form) and, after being selected, send confirmation of travel arrangements before July 15th.


  • Anna Kreshuk – computer scientist @Heidelberg Collaboratory for Image Processing/Uni Heidelberg, Germany
  • Bertrand Vernay – (local organizer of the Edinburgh event), Facility head of Imaging Center @ MRC Centre for Regenerative Medicine, Edinburgh, UK.
  • Fabrice Cordelières – BioImage Analyst & Microscopy Specialist @ CNRS/Bordeaux Imaging Center, France
  • Graeme Ball – Bioimage Analyst @Univ Dundee/School of Life Sciences, UK
  • Irene Fondon – Professor of Signals and Systems @University of Seville, Spain
  • Jean-Marie Burel – Senior Software Architect @OMERO project, Univ Dundee, UK
  • Jean-Yves Tinevez, Analyst & Developer of TrackMate @ Pasteur Institute – Paris, France
  • Jonas Øgaard– Bioimage Analyst @RIIM – Oslo University Hospital, Norway
  • Kota Miura – Image Analyst @University of Heidelberg, Germany & NIBB, Okazaki Japan
  • Sébastien Herbert – Bioimage Analyst @Institut Pasteur, France
  • Patricia Garcia-Canadilla – Bioimage analyst @Institute of Cardiovascular Science UCL, UK
  • Peter Bankhead – Image Analyst, Senior Lecturer in Digital Pathology at Univ. of Edinburgh. & creator of QuPath, UK
  • Petr Walczysko – Software Specialist @OMERO project, Univ Dundee, UK
  • Virginie Uhlmann – PI @EMBL-BI – Heidelberg, Germany

Brief programme

morning coffee-breaks @10:00, lunch @12:00, afternoon breaks @16:00

Day 1 “Scripting in ImageJ”

  • 8:00-8:30 Welcome
  • Introduction to IJ macro language
  • Seminar by Virginie Uhlmann
  • Automated workflows for processing, segmentation and measurement
  • Batch IJ macro
  • 19:00…free night


Day 2  “Scripting in ImageJ”

  • 8:30 3D Tube/filament analysis with ImageJ
  • Seminar by Anna Kreshuk
  • Cells tracking workflow with MaMuT
  • 19:00…free night



Day 3 “Scripting in MatLab”

  • 8:30 Intro to MATLAB; Image processing
  • Seminar by Pete Bankhead
  • 2D & 3D visualization and analysis workflows
  • Integration with OMERO
  • Discussion of advanced workflows
  • Gala Dinner
Day 4 “Work on own data”

  •  9:00…
  • Seminar by Kota Miura
  • Present your problem, model your workflow, work on own data
  • Show your results
  • 19:00 School finishes!


What is , and what is not, included?

  • UPDATE: Trainees are NO LONGER requested to bring their own laptops (local organizers were able to secure a room with workstations for all students)
  • All trainees are provided with coffee breaks, lunch and 1 gala dinner (other dinners NOT included)
  • All course materials will be provided in electronic format
  • Travel & accommodation NOT included (see below how to travel to venue and hotels nearby)

Venue & contacts

TS9 will be hosted by MRC Centre for Regenerative Medicine/Imaging facility
SCRM Building, University of Edinburgh
Edinburgh bioQuarter, 5 Little France Drive
Edinburgh – EH16 4UU

Event Map


Local Organizers

  • Edinburgh: Bertrand Vernay (Bertrand.Vernay@ed.ac.uk)
    MRC Centre for Regenerative Medicine, Univ. of Edinburgh
    Edinburgh bioQuarter5 Little France DriveEdinburgh, EH16 4UU
    Office: +0044 (0)131 651 9543
  • Dundee (Admin) : Graeme Ball (g.ball@dundee.ac.uk)

Staff Training School programme:


Travel & Hotel info:

How to get to Edinburgh


Map of Little france Campus: https://www.ed.ac.uk/maps/maps#proxy_map-proxy

Class rooms (Chancellor’s Building): https://www.ed.ac.uk/maps/maps?building=chancellors-building#main-content

Lunch (Scottish Centre for Regenerative Medicine): https://www.ed.ac.uk/maps/maps?building=SCRM

Auditorium A (Chancellor’s building, 262 seats)

How to get to the Little france Campus

Buses from city centre: #8, #33, #49


Staying in Edinburgh (suggested hotels)

Recommended Accommodation

The Local organisers recommend the Edinburgh University Accommodation (https://www.edinburghfirst.co.uk/for-accommodation/) for attendees and trainers

Guests can simply call/book online using the 15% discount code ‘EVENT’ for a reduction.

Location: Mason house and Salisbury Green are located on the same campus as the venue for the Gala diner and only a 10-15 mins bus ride from the training school venue.

Richmond place accommodations are a 15-20 mins bus ride from the training school venue, and 5 mins away from the Gala diner venue by bus.

 There are 2 other Edinburgh First properties located at Richmond Place. 


(The hotels below are more expensive)

Old Town Chambers

Edinburgh University have a 12% discount in place, which is discounted off the best available rate.  The code is EUNI12, which just needs to be typed in to the “promo code” section when booking: http://www.lateralcity.com/

Hotel Du Vin Edinburgh

2018 Rates – 10% off Best Available Rate between Sunday to Thursday on standard double room. Hotel du Vin also offer a 10% discount on a la carte dining on lunch or dinner between Sunday and Thursday. To book please contact Carol Cairns on 0131 247 8964, or email carol.cairns@hotelduvin.com, saying that you are booking for the University of Edinburgh.

Jurys Inn Edinburgh

Jurys Inn offer the below rates for University of Edinburgh for 2018.

Rates: £93BB – Double for sole occupancy, £10 supplement for double occupancy (Wi-Fi is included complementary)

To book please call – 0131 200 3300 confirming that you would like to book under the University of Edinburgh corporate rate.

Marriott Residences Quartermile

Rates for Marriott Residences Quartermile are listed below. Bookings can be made by calling 0131 229 7150, or you can email david.russell@marriotthotels.com / ri.ediri.reception@marriott.com

Studio for 1-11 nights £122.00 per night; Superior Studios are available for a £10 supplement on rooms at all the above periods

If standard studios are not available during busy periods Marriott may not be able to offer the above rates, but will endeavour to offer a discounted rate for other rooms from what they are selling as standard


The local organizers welcome you to Edinburgh!

Travel Grants

NEUBIAS will offer 7 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. We typically provide less than 1/3 of the grant applications received, so any documented information provided to demonstrate why you need a travel grant is important for us to fully assess your request. 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. Please be aware that grants can only be executed AFTER the Training School (daily signature on attendance sheets compulsory for grantees). The grants are attributed at a fixed rate (TBD) 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 facility “Staff” 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 here to access registration form…