!NEW 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
  • Number of available trainers to assist: >10
  • Application deadline: TBA
  • Selection of candidates: TBA


    • 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 edition here…


    • Applicants should have own data to bring to the school which they have started already analyzing, 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 before June 2nd – follow link at end of this page
    • Should be able to bring own laptop: >=4Gb RAM, 10Gb HD space, ethernet port and 1Gb GPU (please make sure to select correct option in form!) – we are working on a solution for trainees who absolutely cannot bring their own laptops!
    • 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!


  • TBA


(Morning coffee breaks @10:30, lunch at @12:30, afternoon breaks @16:00 and dinners at ~19:30)

Day 1 “Using IJ for Scientific Illustration”

  • 8:30 Welcome
  • 9:00 Introduction to ImageJ: basic operations
  • Checking and preserving the quantitative intensity content of your images
  • Working with color images and images in color
  • From pixels to microns: ROIs & simple measurements, 2D time-series.
  • Assembling data for publication using FigureJ
  • Ethics in DIP

Day 2 “Using IJ for Image Analysis, building workflows”

  • 9:00 Working with pixels: filters, morphomaths and binary operations
  • Working with stacks: 3D image visualisation
  • Seminar: “Lightsheet Image Reconstruction and the Application to Whole Organism Transcription Imaging” 
  • Working with objects: measurements in 2D and 3D
  • Recording simple macros for batch processing; from workflows to macros

Day 3 “Building Image Processing Pipelines with CellProfiler

  • 9:00 Building a pipeline with CellProfiler: basics
  • object detection and feature measurements
  • Machine learning using CellProfiler Analyst
  • New functionalities in CellProfiler 3.0: analysis of 3D data

Day 4 “Choose your toolbox, Work on your data and Present your results”

  • 9:30 Work on own project
  • Present and discuss results
  • 18:00 School ends!

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)?