Core Facilities Session

Registration for elmi2021 includes the Core Facilities session; no additional registration is required.

Core Facilities Session

Tuesday 22 June 2021, this session was included with elmi2021 registration.

Schedule (CET):

10:00 Welcome
10:15 Session 1: Crib Talks
11:15 Coffee
11:30 Session 2: Data Processing and Infrastructure
12:30 Online Games: Scribble
13:00 Aerobics
13:30 Lunch
14:15 Session 3: Online Tools for Core Facilities – towards a global searchable database
15:15 Coffee
15:30 Session 4: Introduction to QUAREP-LiMi and Progress Report
17:00 Covid lessons and general discussion/Corona beer hour/group discussion with an option for breakout rooms

Session 1: Crib Talks

Session Chairs

Six Crib Talks of seven minutes each were given as follows: 

1.  Christiane Peuckert, Stockholm, Sweden

2.  Pascal Lorentz, Basel, Switzerland

3.  Mariana Carvalho, Braga, Portugal

4.  Radek Machan, Singapore

5.  Herlinde De Keersmaecker, Ghent, Belgium

6.  Ralf Palmisano, Erlangen, Germany

The talks were to help to identify common themes of facility operation and will widen community awareness of core facilities outside of the more well known facilities that we often hear from.

The session ended with an open forum with advice and opinions given from the floor.

Session 2:  Data Processing & Infrastructure:  Shoulda, Woulda, Cuda?

Session Chairs

Advances in bioimaging techniques come along with the acquisition of more data/larger files.  Consequently, the explosion of produced data requires additional evaluation of the needs for structured and mineable imaging data infrastructures.  IT-infrastructure requirements might differ between institutions and/or core-facilities due to size, available technologies and user demand.  Nevertheless, we can learn from each other in 'how to' optimize data transport, data storage, image analysis infrastructure, software training and curation by exchanging experiences and insights.

This interactive session consisted of two parts with the aim of exchanging ideas on how to best set up the (image-) data infrastructure in a microscopy facility.  What is needed, how do others organise data infrastructure and what would you do (different) if you could start all over again?

Interactive participation was invited by sharing experience, insights and questions:  Shoulda, Woulda, Cuda ...

The panel members for this session were:

Gopi Shah (Mesoscopic Imaging Facility, EMBL Barcelona, Spain)

Anna Klemm (BioImage Informatics Facility, SciLifeLab, Uppsala, Sweden)

Kurt Anderson (Crick Advanced Light Microscopy, Francis Crick Institute, London, UK, )

Timo Zimmermann (EMBL Imaging Centre, EMBL Heidelberg, Germany)

Session 3:  Useful Online Tools for Core Facilities:  Towards a Global Searchable Database

Sessions Chairs 

Many of us Core Facility people end up making videos to show how to use a function on a microscope or teach a topic to students in a course.  This is time consuming, but once the video is done, a lot of time is saved, especially if it can be used by the community.  This is also true for other useful tools for Core Facilities.

There are already very useful online resources available, but it is not always straightforward to find them.  For example a google search either lists too many options and it is hard to find the best/right link or most of the search results do not fit. 

The aim of this session was to investigate the community interest in a searchable, up to date database of online resources for microscopy and discuss the organization (how to keep it up to date, host domain…).  During the session the audience helped to collect existing online resources.

Introduction and short talks by:

Jennifer Waters, Director of the Nikon Imaging Center at the Harvard Medical School & a Chan and Zuckerberg Initiative Imaging Scientist:

Talley Lambert, Lecturer in Systems Biology at the Harvard Medical School, Associate Director of Imaging Technology in the Nikon Imaging Center: FPbase: a community editable fluorescent protein database

Gleb Grebnev, Training Programme Manager, EMBL, Global Bioimaging, Chan and Zuckerberg Initiative funded: Global BioImaging Training Resource: community-driven curated resource for imaging scientists around the globe

Followed by discussions in 3 Break out sessions with the option for feedback via shared documents. The documents will be available for information and feedback also after the CF session. Moderators presented a short wrap up of their breakout session.

Session 4:  QUAREP-LiMi

Session Chairs

A.  QUAREP-LiMi - General overview about the initiative:  Aims, Members, Organisation, Working Groups, Networking, Current and Future Activities (Roland Nitschke, Freiburg) (15 minutes).

B.  Selected QUAREP-LiMi Working Groups (WG) (60 minutes)  

  1. WG 1 – Illumination Power (Laurent Gelman, Basel)
  2. WG 4 -  System chromatic aberration and co-registration (Hans Fried, Bonn)
  3. WG 7 - Metadata (Caterina Strambio De Castillia, Worcester)
  4. WG 11 – Microscopy Publication Standards (Paula Montero Llopis, Boston)

C.  Report about the QA Paper of the French RTmfm Metrology Group (Orestis Faklaris, Montpellier) (15 minutes)