Core Facilities Session

Taking place on Tuesday 22 June 2021, this session is included with elmi2021 registration, we look forward to seeing you there.

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 will be given as follows: 

1.  Christiane Pueckert, 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 will 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 will end 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 consists of two parts where we aim to exchange 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?

We are looking forward to your interactive participation by sharing your experience, insights and questions:  Shoulda, Woulda, Cuda ...

The panel members for this session are:

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 is 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 will help us collect existing online resources.


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)

All presentations might include on-line polls and surveys.



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