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A high content confocal microscope for fast 3D imaging of living samples

English title A high content confocal microscope for fast 3D imaging of living samples
Applicant Pertz Olivier
Number 177096
Funding scheme R'EQUIP
Research institution Departement Biomedizin Universität Basel
Institution of higher education University of Berne - BE
Main discipline Cellular Biology, Cytology
Start/End 01.10.2018 - 31.03.2020
Approved amount 349'840.00
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Keywords (4)

image analysis; high content screening; live cell imaging; confocal 3D imaging

Lay Summary (French)

Dans la derniere decennie, les progres en biologie ont ete revolutionnes par le development de nouvelles technologies qui permettent d’analyser la dynamique de processus cellulaire avec un haut debit. Quand ces dernieres sont couplee avec des techniques modernes d’analyses automatique d’image et de statistique, ces nouvelles technologies permettent une analyse beaucoup plus large des systemes biologique.
Lay summary
Ce projet consiste en une infrastructure d’equipement de microscopie qui permet d’analyser des systemes biologiques en 3 dimensions avec un tres haut debit. La rapidite du systeme permet d’analyser des systemes cellulaires vivants, et donc d’explorer la dynamique de systemes cellulaires vivants. Des serveurs pour le stockage de donnees, et d’analyse du grand volume de donnees sont aussi inclus dans ce systeme, qui sera situe dans l’Institut de Biologie Cellulaire de l’universite de Berne. Le systeme sera aussi mis a disposition d’autres instituts/facultes. Le potential de cet equipement est de democratizer l’analyse a haut debit de systemes cellulaires a l’Universite de Berne.

Direct link to Lay Summary Last update: 22.08.2018

Responsible applicant and co-applicants

Associated projects

Number Title Start Funding scheme
153280 Composition of different BicD/ mRNA complexes and function of cytoplasmic Cbp80 01.07.2014 Project funding (Div. I-III)
160264 Mitochondrial biogenesis in Trypanosoma brucei 01.05.2015 Project funding (Div. I-III)
159320 Deciphering the Function of Genome Nuclear Organization in Cell Fate Determination (prolongation) 01.09.2015 SNSF Professorships
173188 Drosophila BicD family members: mitotic functions, structural aspects of RNA localization, and functional characterization of a novel member 01.11.2017 Project funding (Div. I-III)
176008 Hunting for natural products targeting aberrant proliferative signaling in melanoma 01.01.2018 Project funding (Div. I-III)
176226 Mechanisms of gene regulation by chromatin compaction 01.10.2017 Project funding (Div. I-III)
156869 Mechanisms of PARP inhibitor resistance of BRCA2-deficient mouse mammary tumors 01.08.2015 Project funding (Div. I-III)
163061 Mapping Rho GTPase signaling networks through acute, dynamic stimulation of spatio-temporal signaling fluxes. 01.04.2016 Project funding (Div. I-III)
182465 Pathogen-host cell interactions during the liver stage of Plasmodium parasites III 01.01.2019 Project funding (Div. I-III)
159519 Pathogen-host cell interactions during the liver stage of Plasmodium parasites 01.08.2015 Project funding (Div. I-III)


In the last decade, our understanding of biology has been revolutionized by development of new microscopy technologies which allow us to image the dynamics of cellular processes in single living cells. Recently developed automatized microscopes parallelized imaging of cells to a yet unattained throughput. Coupled with automated image analysis and adequate statistic methods, we are now in position to extract meaningful, biologically relevant information from these high content screening (HCS) microscopy datasets. Thus, these techniques permit comprehensive interrogation of biological objects, enabling for a system-view of cellular processes. While most HCS datasets were acquired using classic 2D adherent cell systems and epifluorescence microscopy devices, biological systems are intrinsically three-dimensional. Recent advances in confocal fluorescence microscopy now allows rapid optical sectioning necessary to complex live 3D objects such as organoids, small embryos, tissue explants or even entire animals. Here, we apply for funds to acquire a fast spinning disk confocal microscope with HCS capabilities. Rapid 3D imaging of live samples will allow HCS imaging of dynamic processes at high-resolution for systematic chemical or reverse genetic screens. This is a flexible, state of the art equipment that will cover different needs at the Institute of Cell Biology (ICB) and the University of Bern (UniBE). A data handling system to perform “big data” analysis of the imaging datasets is also included.The Pertz lab will perform HCS live imaging of signaling activities of 3D cancer organoids with single cell resolution, capturing heterogeneous pathological signaling states that underlie the process of cancer drug resistance with high experimental throughput. This might have an important impact for personalized medicine. The Heussler lab has recently initiated a high throughput gene knockout project to identify malaria parasite genes required for parasite development in hepatocytes. HCS will provide the necessary throughput to timelapse the infection process of more than 200 already identified knockout parasites. The Suter lab will use the microscope for live cell imaging of cell division in the Drosophila embryo. Compared to currently accessible point-based scanner confocal microscope, the speed and large field of view will enable to visualize the dynamics of this process in a high number of cells in the embryo. The Meister lab will use the HCS microscope to perform genome-wide RNAi screens to characterize molecular players of dosage compensation in C. elegans. The Rottenberg lab will visualize cell cycle dynamics in single living cells during the acquisition of cancer drug resistance. The Ochsenreiter lab will perform image-based RNAi screens to identify new genes important for mitochondrial genome segregation in trypanosomes. Having such a HCS microscope at ICB and UniBE in general, would cover important needs for 3D fluorescence live imaging, as well as HCS experiments. The combination of a HCS compatible microscope and robust infrastructure and pipelines for data analysis, has the potential to democratize HCS screening experiments at UniBE. This is expected to provide a boost in competitivity to the ICB and UniBE in general.