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The "Community Workshops" are the signature session of SPAOM and they aim to feature balanced sessions made of a mix talks and hands-on demos, given by scientists to scientists, and mostly focusing on imaging techniques, tools, sample prep, hints, shareable projects, protocols, open source etc... 

The SPAOM2021 edition will include 4 Community Worshops with the themes:

(all times in WET - Lisbon local time [+1h in Spain!]). 

Frugal Bioimaging (Nov 23rd, 11:00-12:00)

The Frugal Bioimaging workshop aims to present two hands-on communications of two open-source devices by providing some detail on the practical aspects of the usability of such systems and a DIY approach to build them. 

  • OpenScope & OpenFrame platforms (Paul French & Sunil Kumar) - 30min
  • PlanktonScope:Frugal high-throughput imaging of ocean microbes at planetary scale (Anna Oddone & Thibaut Pollina) - 30min

High-throughput & high-content screening microscopy (Nov 23, 17:00-18:00)

This workshop will present fundamental aspects of high content screening (HCS), ranging from sample preparation, instrumentation, image acquisition and batch image analysis. The quantification of a HCS dataset will be exemplified using open source image analysis tools: CellProfiler and KNIME.

  • "HCS sample preparation" (Hugo Botelho & André Maia) - 10min
  • "High-throughout analysis workflows in CellProfiler (Beth Cimini) - 25min
  • "High-throughout analysis workflows in KNIME " (Marc Bickle) - 25min

Machine Learning in Bioimage analysis (Nov 24th 11:00-12:00)

  • "3D tiles and automated tracking" (Sebastien Tosi) - 30min
  • "Automatic cell tracking using StarDist and Trackmate" (Elnaz Fazeli) - 30min

Community proposed (Nov 24th 17:00-18:00) 

  • Phototoxicity: Light, the silent killer (Philippe Laissue + Claire Brown) - 30min
  • Remote access & trianing tools for imaging (Johanna Bischof) - 30min


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