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. SPAOM2021 will include 4 Community Worshops with the themes:
(all times in WET(=GMT) - Lisbon local time [+1h in Spain and central Europe!]).
Frugal Bioimaging (Nov 23rd, 12:00 GMT 60min)
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
- PlanktoScope: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 GMT, 60min)
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
Community proposed (Nov 24th 17:00 GMT, 60min)
- Phototoxicity: Phototoxicity: Sources, assessment and reduction (Philippe Laissue + Claire Brown) - 30min
- Remote access & trianing tools for imaging (Johanna Bischof) - 30min
3D Tile &Stitching + Automated Cell Tracking (Nov 25th 12:00 GMT, 60min)
- "MosaicExplorerJ: Interactive Stitching of Terabyte-size Tiled Datasets from Lightsheet Microscopy" (Sebastien Tosi) - 30min
MosaicExplorerJ is an ImageJ macro to explore, align and stitch 3D TIFF tiles coming from microscopy datasets acquired as tiled scans (aka ‘Mosaics’). It does not require any data format pre-conversion and can handle datasets coming from dual-camera detection and dual-side illumination lightsheet microscopes. The whole procedure does not rely on any automated method and can be performed interactively, which brings a direct readout on the quality of the alignment and potentially help to identify issues such as optical misalignments or sample movements during acquisition.
In this workshop, we will discuss the pre-requirements and features of the software, cover its setup, and perform the stitching of large tiled datasets acquired by a custom lightsheet microscope used to image large optically cleared samples.
Tosi S, Bardia L, Barallobre MJ et al. MosaicExplorerJ: Interactive stitching of terabyte-size tiled datasets from lightsheet microscopy [version 2; peer review: 2 approved]. F1000Research 2021, 9:1308
"Automatic cell tracking using StarDist and Trackmate" (Elnaz Fazeli) - 30min
This year, SPAOM will also include a session with Imaging/Microscopy Community Networks (Nov 24th at 14:15 GMT [+1h in Spain & central Europe]). It is our please to acknowledge the participation of (by order of appearance):
EuroBioimaging/Global Bioimaging - presented by Antje Kepler
PPBI - Portuguese Platform for Bioimaging - presented by Gaby G Martins
REMOA - Red Espanõla de MIcroscopia Óptica Avanzada - presented by Maria Calvo
NEUBIAS Academy - presented by Rocco d'Antuono
COMULIS COST Action - presented by Erin Tranfield
FocalPlane - presented by Esperanza Agullo-Pascual
QUAREP LiMi - presented by Roland Nitschke