mesoSPIM User Meeting 2022 poster

mesoSPIM User Meeting: Thursday, March 10th, 2022

The User Meeting was held fully online via Zoom, with 209 registered participants from all over the world!


Time Talk
9:00-9:15 Welcome by Fritjof Helmchen, UZH
Session 1 Clearing techniques. Moderator: Nikita Vladimirov
9:15-9:35 Alba Vieites Prado (Renier Lab, ICM) iDISCO+ tissue clearing and ClearMap for the analysis of axonal projections and brain vasculature.
9:40-10:10 Etsuo Susaki (Juntendo University) CUBIC for whole-organ/body cell circuit and tissue architecture analysis.
10:15-10:35 Shan Zhao (Bodenmiller Lab, UZH) The challenges of human tissue clearing, imaging and application.
10:40-11:00 Sven Hildebrand (Roebroeck Lab, Maastricht University) Investigating the human neocortex in 3D: Approaches for imaging angioarchitecture, cytoarchitecture, and intrinsic cortical connectivity.
11:00-11:15 Break
11:15-12:00 Nikita Vladimirov (Helmchen Lab & ZMB, UZH) Demo of a mesoSPIM workflow.
12:00-13:00 Lunch break
Session 2 Developers: current status and outlook. Moderator: Philipp Bethge
13:00-13:20 Fabian Voigt (Engert Lab, Harvard) Mollusc-inspired microscope objectives for imaging cleared tissue.
13:20-13:40 Nikita Vladimirov (Helmchen Lab & ZMB, UZH) mesoSPIM development and updates.
Session 3 Facility managers and power users: experiences and challenges. Moderator: Fabian Voigt
13:40-14:00 Laura Batti (Wyss Center) ALICe: Advanced Lightsheet Imaging Center.
14:00-14:20 José María Mateos (ZMB, UZH) Experiences running the MesoSPIM in a Core Facility
14:20-14:40 Anna-Maria Reuss (Aguzzi Lab, USZ) mesoSPIM imaging and handling of large human data sets
14:40-15:00 Thomas Naert (Lienkamp Lab, UZH) mesoSPIM and U-Net deep learning: three-dimensional modeling of embryonic development and disease
15:00-15:15 Break
Session 4 Image processing and visualization. Moderator: Nikita Vladimirov
15:15-15:35 Stephan Preibisch (HHMI Janelia) Towards reconstruction of peta-scale lightsheet microscopy datasets
15:35-15:55 Peter Majer (Oxford Instruments/Bitplane). Imaris and lightsheet data analysis. What works well ()
15:55-16:15 Benjamin Schmid (OICE) Intuitive rendering of 3D animations from microscope data using 3Dscript, locally and on a server.
16:15-16:35 Johannes Paetzold (Ertürk Lab, TUM) Machine learning for vascular structures in microscopic data.
16:35-16:45 Break
16:45-17:30 Virtual round table: Extended Q&A, discussion, current problems and future directions. Moderator: Philipp Bethge.


The talks are now posted on mesoSPIM YouTube channel. Some talks are edited or omitted at the speaker’s request due to confidential information (a no-publish request). Thank you for understanding!