TS8 Edinburgh 2018

4th Training School for Early Career Investigators (TS8), 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: June, 1st week
  • Payments must be processed before July 15th!


    • Principles, techniques and ethics of digital image processing (DIP); publication of bioimages.
    • Building practical workflows to analyse 2D, 3D & time-lapse bioimages
      (eg. object segmentation and densitometry, spot detection & tracking or filament tracing)
    • Introduction to workflow automation: record & reuse commands, scripting of workflows/pipelines
      NOTE – if you work on an imaging facility and are already familiar with the basics of DIP & analysis check the school for “Staff” in the same dates & venue, which is focused on scripting of workflows.
    • Extracting and validating quantitative numerical data from bioimages
    • Solve your own problem, code your workflow and explore different tools with help from Analysts

    More info & testimonials about previous editions here…


    • Applicants should have own data to bring to the school which they have started analysing, and be able to explain what they need to learn about image analysis to advance their research (explained in application form) –  some basic-level experience with a tool like ImageJ is advisable, but not required.
    • Must fill valid application form (link at the end of this page) BEFORE the deadline (see above)
    • UPDATE: Trainees are NO LONGER required to bring own laptop!
    • Must include brief letter of motivation (text pasted into registration form), 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/times of the course (no exceptions!)
    • Must be able to bank-transfer administrative charges (credit card or paypal not possible).
    • Must comply to administrative conditions and confirm travel&hotel by 26 of July – read conditions at end of application form!

Trainers (more being confirmed!)

  • Anna Klemm – Staff Scientist @Center for Image Analysis / SciLifeLab, Uppsala, Sweden
  • Anna Kreshuk – computer scientist @Heidelberg Collaboratory for Image Processing/Uni Heidelberg, Germany
  • Fabrice Cordelières – BioImage Analyst & Microscopy Specialist @ CNRS/Bordeaux Imaging Center, France
  • Graeme Ball – Bioimage Analyst @Univ Dundee/School of Life Sciences, UK
  • Kota Miura – Image Analyst @University of Heidelberg, Germany & NIBB, Okazaki Japan
  • Laura Murphy – Image Analyst @IGMM Advanced Imaging Resource, Edinburgh UK
  • Laure Plantard – Imaging Specialist@LMF, Max Planck Institute – CBG, Germany
  • Peter Bankhead – Image Analyst, Senior Lecturer in Digital Pathology at the University of Edinburgh & creator of QuPath, UK
  • Robert Haase Bioimage Analyst @MPI-CBG, Germany
  • Virginie Uhlmann – PI @EMBL-BI – Heidelberg, Germany

Brief programme (preliminary)

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

Day 1 “Using IJ for Scientific Illustration”

  • 8:30 Welcome…
  • Intro to ImageJ: basic operations
  • Checking & preserving quantitative intensity content of your images
  • Colour images
  • Seminar by Virginie Uhlmann
  • From pixels to microns: ROIs & simple measurements, 2D time-series.
  • Working with stacks: 3D viz
  • Assembling data for publication (FigureJ)
  • free night
Day 2 “Using IJ for Image Analysis, building workflows”

  • 8:30 Working with pixels: filters, morphomaths and binary operations
  • Working with objects: Measurements in 2D and 3D
  • Seminar by Anna Kreshuk
  • Recording simple macros for batch processing
  • From workflows to macros
  • free night
Day 3 “Building Pipelines with CellProfiler & QuPath

  • 8:30 Building a pipeline with CellProfiler
  • Cell profiler Analyst
  • Seminar by Pete Bankhead
  • QuPath
  • Gala dinner
Day 4 “Choose your toolbox, work on own data & present results”

  • 8:30 Work on own data
  • Seminar by Kota Miura
  • Present and discuss results
  • 18:00 School ends!

What is, and what is not, included?

  • Trainees are requested to bring their own laptops (if you cannot bring a laptop please indicate so in application form). We have a limited number of workstations available fpr trainees who absolutely cannot bring their own laptop.
  • Once accepted we will contact you with instructions to install all materials
  • All trainees are provided with coffee breaks, lunch and 1 gala dinner (other dinners NOT included)
  • Travel & accommodation are not included for trainees (see below how to travel to venue and hotels nearby).

Venue & contacts

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

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 phone# : +0044 (0)131 651 9543
  • Dundee (+Admin): Graeme Ball (g.ball@dundee.ac.uk)

ECI 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 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 “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 here to access registration form…