External meetings, courses & surveys in the field

Machine Learning for Image Analysis

Course Overview

This is a blended learning course on Machine Learning for Image Analysis, consisting of three online sessions with associated hands-on exercises prior to the workshop, a three day face-to-face workshop at EMBL Heidelberg and two optional online sessions with associated hands-on exercises after the workshop. The course is jointly organised by CORBEL, EMBL, German BioImaging and NEUBIAS (COST Action CA15124).

The course will be a great mix of intensive learning, extensive hands-on and community networking in the field of Machine Learning for Image Analysis.

Up-front online sessions: Participants will review the fundamentals of machine learning in three up-front webinars complemented by online tutorials. The webinars will take place on 2nd, 9th and 16th October 2018, 12:00 – 14:00 but a recorded alternative can be provided.

On-site workshop: Next, they will apply their knowledge at an on-site workshop (EMBL Heidelberg, October 29-31), in small interactive groups (the workshop has 20 available seats and ~8 trainer/lecturer), to both reference datasets and their own data. Topics to be practiced in these groups include: 2D and 3D segmentation with convolutional neural networks, Content aware image restoration, simulation of ground truth data, labeling strategies and transfer learning. Participants will be asked to pick one group for the practical sessions.

Follow-up online sessions (optional): After the on-site workshop, two optional advanced training webinar, complemented by a online tutorials, will be given on 9th and 16th November 2018. These will focus simulation of data, transfer learning and boosting.

Application deadline: June15 2018

For additional information please visit the course webpage: https://www.ebi.ac.uk/training/events/2018/machine-learning-image-analysis


Maastricht Microscopy Meeting (M3) on Advanced Optical Microscopy

Friday 15 June, 2018

For information and registration visit here


Stereology Workshop at the Institute of Anatomy, University of Bern, Switzerland

August 20th – 24th, 2018 and August 25th & 26th 2018 (newCAST training)
Information and registration on www.stereology.unibe.ch
This course provides an introduction to stereology and focuses on its practical
application in biomedicine. It covers experimental design, sampling and use of
stereological probing.
The program includes lectures, exercises and laboratory demonstrations.
2nd Part: Hands-on VISIOPHARM newCAST: Sat 25.08 & Sun 26.08.2018


CMI Imaging in the Life Sciences (ILS) Meeting 2018

BioImaging Austria/CMI, Sep 20 & 21, Vienna BioCenter Campus

The CMI Imaging in the Life Sciences (ILS) Meeting 2018 is organized by BioImaging Austria-CMI and will take place on September 20th & 21st at the Vienna BioCenter Campus, Research Institute of Molecular Pathology, IMP Lecture Hall. Follow this link for more information, registration for the ILS Meeting, Lunch Seminars or poster submissions: http://www.bioimaging-austria.at/web/pages/cmi-imaging-meeting.php

Seats are limited; don't hesitate to register or submit a poster abstract by July 15th!

Invited speakers cover a wide range of state-of-the-art imaging technologies and their unprecedented application in the life sciences: Werner Kühlbrandt, Willy Suppato, Monika Ritsch-Marte, Martina Marchetti-Deschmann, Rainer Kaufmann, Florian Schur, Eva Pereiro, Birgit Plochberger, Marcus Hacker, Ulrich Dodt, Wolfgang Graier, Jacky Goetz, Wolfgang Drexler, Thomas Beyer and Ivan Viola.

BioImaging Austria-CMI is very much looking forward to welcoming you to the ILS Meeting 2018!


Workshop on Image Registration & Correlation

BioImaging Austria/CMI is happy to announce its first Workshop on Image Registration & Correlation which is organized jointly with Vetmeduni, VRVis and Thermo Fisher Scientific/AMIRA.

The workshop will take place at Vetmeduni Vienna on June 28th & 29th.

Seats are limited; please register at http://www.bioimaging-austria.at/web/pages/training.php



Are you a life-scientist needing to quantify microscopy images?

Do you want to learn how to automatically detect objects in images, track spots and cells, build reproducible image processing workflows, deconvolve and enhance microscopy images, and handle massive data? If yes, this school is for you!

What you will learn!

In this one-week school you will get a hands-on introduction to Image Processing and Analysis, with an emphasis on biologically relevant examples. You will learn the fundamentals of image analysis, including macro programming in ImageJ/Fiji, scripting in MATLAB, as well as other software solutions and a range of focused topics.

In the first part of the week, we will cover the process of image formation as it pertains to image analysis: Resolution, correct exposure, point-spread functions, detector noise, Shannon's sampling theorem, and aliasing. All with a clear focus on application in the lab.

In the second part of the week we will cover a number of focused topics, building on what was learnt during the first days:

  • Call4Help session
  • Scripting in MATLAB
  • Tracking particles and cells in time-lapse recordings
  • Segmentation and classification via supervised Machine Learning in ilastik
  • De-convolution of microscopy images
  • Stitching and registration of stacks of large image data
  • Working on your own project / data

When: 19th - 24th June 2018

Where: ETH, Zurich, Switzerlan

Participation fee: 500 CHF (academia) / 1000 CHF (industry)

For further information please visit this webpage: http://2018.zidas.org/


Maastricht Microscopy Meeting (M3) on Advanced Microscopy and Vital Imaging, June 15, 2018
The 9thMaastricht Microscopy Meeting on Advanced Optical Microscopy will be held at the Maastricht University Hospital, on June 15, 2018.
Several international speakers will give the latest info on different microscopy and imaging techniques.
Participation is free!
Please email to register secr-mcb@maastrichtuniversity.nl .




The 12th Zurich Summer School on Biomedical Imaging will take place in Zurich, Switzerland, from 3 September - 14 September 2018. 

The school is dedicated to teaching the basics and wider context necessary to understand recent advances and current challenges in biological and medical imaging. Cutting-edge techniques using a wide range of image-formation mechanisms — including magnetic resonance imaging, positron emission tomography, infrared and optical microscopy, electron microscopy and X-ray imaging — will be discussed, with a focus on multimodal and multiscale imaging methods, together with supporting technologies such as computer-aided image analysis and modelling.

The school will provide different tracks for participants with a background in life sciences and physical sciences, respectively. Furthermore, specialized lectures will address current topics in biological and medical imaging. The students will have lectures in the morning and practical sessions in the afternoon (either hands-on lab work or lab demonstrations, depending on the field). The program will be rounded off with a practical day and an industry day.

The school follows a challenging and demanding schedule. It addresses excellent MSc and PhD students as well as scientists from industry with background in biology, chemistry, computer science, engineering, mathematics, medical science or physics. We plan to admit about 60 participants (internally and from abroad).

Admission will be decided based on the applicant’s curriculum vitae, a statement of purpose and applicant’s references. Students who have not yet started a PhD program may apply for a stipend. Interested students are kindly asked to submit their application pack including their study grades and reference letter on our homepage (www.excite.ethz.ch)

The application deadline is Monday, 23 April 2018. The notification of acceptance will be given by 25 May 2018.

Further information can be found here: www.excite.ethz.ch





Call for proposals - Advaned Imaging Center @Janelia

The Advaned Imaging Center (AIC) makes imaging technologies developed at Janelia available to the scientific community before the instruments can be purchased commercially. Scientific investigators from nonprofit organizations anywhere in the world may apply to use the facility.  AIC is now accepting proposals from scientists who would like to conduct experiments at their facility at Janelia Research Campus. The deadline to submit a proposal is June 15, 2017. Under the program, visiting scientists will spend 1-2 weeks (or longer if there is justified scientific reason) at Janelia to conduct experiments on a microscope with the support of the AIC team. The currently available microscopes are:

  1. Interferometric Photoactivated Localization Microscope (iPALM)
  2. Aberration-corrected Multifocus Microscope (acMFM)
  3. Lattice Light Sheet Microscope (2nd generation Bessel Beam Microscope)
  4. Live Cell Multicolor Structured Illumination Microscope (SIM)

Scientists whose proposals are selected are responsible for travel arrangements to Janelia. The Janelia Visitor Program will cover the cost of lodging for the visiting scientist, basic experimental reagents, technical support from our applications scientists, and scope time.

To learn more about this call, please click here.


West-Life VRE looks for collaborators for participation in an online survey

West-Life is an electronic infrastructure initiative (Virtual Research Environment, VRE) to support the use and analysis of structural biology data using advanced computational methods. They are now carrying out a survey to collect information that will guide their efforts to extend the exploitation of structural biology to other scientific communities, also by providing the data in a convenient form, with adequate software support and focusing on what would be most useful. 

The survey contains eight questions and should not take more than five minutes of your time. Please visit:




RItrain Staff Exchange open call

The RItrain project is organising staff exchange programme visits as part of its mission to share management expertise among European Research Infrastructures.

The purpose of RItrain Staff Exchanges is for managerial staff from European Research Infrastructures to learn from managerial and leadership best practices in areas that are new to them, or that they feel their research infrastructure needs to develop specific expertise in, by making exchange visits to research infrastructures that are noted for their excellence in selected areas.

During 2017 three areas will be piloted:

  1. Stakeholder Management and Community Building” May/June 2017 in Prague/Brno CZ, organised by the Institute of Molecular Genetics, Academy of Sciences Czech Republic (deadline for submission: 31 March 2017). For more information click here
  2. “Strategic Vision, Governance and Business Development” 6 – 7 or 10 – 11 April 2017 in Amsterdam NL, organised by EATRIS-ERIC (deadline for submission: 5 March 2017)
  3. “Service Provision” 2 – 5 May 2017 in Hinxton UK, organised by EMBL-EBI (deadline for submission: 31 March 2017)

If interested please visit the RItrain Staff Exchange webpage

Applicants are requested to submit a motivation statement and a CV as part of their application. As space is limited, applications will be evaluated along criteria specified in the call texts. There are no fees to participate, subsistence is included but selected delegates will need to cover their own travel and accommodation costs. After positive evaluation this programme shall be continued with new calls for 2018 to be published towards the second half next year.


RItrain Master Programme

RItrain, the Research Infrastructure Training Programme, is an EU-funded Horizon 2020 project aimed at improving and professionalising the training of managerial and leadership staff in research infrastructures (RIs). Our vision is to develop a new generation of executives of national and international RIs and equip them with state-of-the-art managerial and leadership skills tailored to scientific services providers.

The Masters programme is tailored for busy executives by organising its 60 ECTS into a mixture of face-to-face and online activities held by international faculty and top managers from RIs. The face-to-face modules last 3-4 days and run over 18 months.

Previous education and experience will be recognised depending on our evaluation and pre-entry assessment.










Euro-BioImaging Stakeholder meetings