Smart microscopy banner

The Euro-BioImaging Industry Board has organized an exclusive 1-day workshop for its members and staff from the Euro-BioImaging Nodes on the subject of “Smart Microscopy” at the Imaging Centre at EMBL, Heidelberg, on Thursday13th October 2022, which was attended by 87 on-site and online participants.

Smart microscopy connects bioimage analysis with computer-controlled microscopy to generate automated and adaptive imaging workflows to enable quantitative, statistically meaningful results in complex biological systems. This approach brings new challenges, such as accessing and controlling instrument hardware via suitable software, designing good workflows or handling of large, terabyte-sized data sets during operation.

The workshop managed to bring together leading instrument and software providers with experts from our Euro-BioImaging Nodes for fruitful discussions around research needs, technical requirements and existing solutions for Smart Microscopy.

Recordings of the Keynote lectures are available on our YouTube Channel.

The workshop participants concluded that the first steps towards standardization and making Smart Microscopy more accessible would be to 

  • Build a consensus on what the field should be called and what is included
  • Agree on a standard ontology for Smart Microscopy and workflow components to be used and adopted across different instrument control and analysis software and define a list of core workflow components that should be accessible in each software
  • Identify the top community needs of microscope users and facilities for smart microscopy (from data format or interoperability issues to technical access requirements)

We would like to discuss this further with the community and collect YOUR input for further discussion with instrument and software producers.

We are looking forward to hearing from you about your opinion on standards and best practices in this emerging field!

Smart Microscopy Workshop 2022


10:00 – 10:10Martin Tewinkel, Evident Olympus and Board Chair
Welcome and short intro Euro-BioImaging Industry Board
10:10 – 10:15Claudia Pfander, Board Coordinator
Meeting agenda and objectives
10:15 – 10:45Rafael Camacho, University of Gothenburg
Good workflow design - Introduction and Keynote
10:45 - 11:00Marc Tramier, MRic facility CNRS/ University of Rennes, France Bio-Imaging Node
The roboscope: smart automated microscopy using real time embedded artificial intelligence combining microscopy control
11:00 - 11:15Evangelis Sisamakis, PicoQuant GmbH
FLIM, FCS and single molecule FRET workflows in Luminosa, the new single photon counting confocal microscope by PicoQuant
11:15 - 11:30Laurent Thomas, Acquifer
High-throughput imaging with the ACQUIFER Imaging Machine: versatile scripting opportunities
11:30 - 11:45Christoph Greb, Leica Microsystems
AI-based ROI Definition for Laser Microdissection
11:45 - 12:30Discussion round
13:30 - 14:00Aliaksandr Halavatyi, EMBL
Tools and software interfaces - Introduction and keynote
14:00 - 14:15Ludovico Silvestri, European Laboratory for Non-linear Spectroscopy
Online correction of sample-induced defocus in light-sheet fluorescence microscopy
14:15 - 14:30Marco Castello, Genoa Instruments - Istituto Italiano di Tecnologia
Carma: an FPGA-based microscopy platform for (image) scanning microscopy
14:30 - 14:45Giacomo Mazzamuto, National Research Council - National Institute of Optics (CNR-INO) and LENS
Tools and strategies for high-throughput light-sheet Fluorescence Microscopy
14:45 - 15:30Discussion round
16:15 - 16:45Antonio Politi, MPI Göttingen
Feedback microscopy and data analysis
- Introduction and keynote
16:45 - 17:00Kees Jalink, Netherlands Cancer Institute (Euro-BioImaging Functional Imaging Node)
Adapting high-content microscopy screening to study dynamic signaling mechanisms
16:00 - 17:15Manoel Veiga Gutierrez, EVIDENT Technology Center Europe GmbH
Workflow for analyzing high-content microscopic image data
17:15 - 17:30Roman Zinner, Carl Zeiss Microscopy GmbH
Data Storage and Processing Server
17:30 - 17:45Alberto Diaspro, UNIGE-IIT
The intelligent microscope
17:45 - 18:30Discussion round