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spim4You

spim4You: customised solutions for light sheet microscopes and imaging data analysis.

Total Cost €

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EC-Contrib. €

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Partnership

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Project "spim4You" data sheet

The following table provides information about the project.

Coordinator
MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV 

Organization address
address: HOFGARTENSTRASSE 8
city: MUENCHEN
postcode: 80539
website: n.a.

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Germany [DE]
 Total cost 148˙613 €
 EC max contribution 148˙613 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2015-PoC
 Funding Scheme ERC-POC
 Starting year 2015
 Duration (year-month-day) from 2015-11-01   to  2017-04-30

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    MAX-PLANCK-GESELLSCHAFT ZUR FORDERUNG DER WISSENSCHAFTEN EV DE (MUENCHEN) coordinator 148˙613.00

Map

 Project objective

Biological research heavily relies on visualization of biological samples by microscopy. In recent years light-sheet microscopy has emerged as a paradigm shifting technique. Only with light sheet microscopy it is for instance possible to follow every cell in a living system throughout development, to monitor brain activity of a live animal or to study cancer cells in their native three dimensional environment within an organism. Thus, light sheet microscopy has the potential to revolutionize biological research and in the near future every research establishment will have a light sheet microscope. During the Hourglass ERC grant, my laboratory developed two widely used open access solutions for light sheet microscopy:

1.) OpenSPIM, a modular open hardware platform that enables anyone to construct and operate a simple light sheet microscope and 2.) a powerful library of open source software solutions to process and analyze lights sheet microscopy data.

Together, these tools form a powerful foundation for exploiting the spectacular benefits of light sheet microscopy for research. The problem is however that in order to use light sheet microscopy a formidable set of expertise spanning physics, engineering, computer science and biology is required and only very few research laboratories have this level of interdisciplinary skills. The idea of our Proof of Concept proposal is to leverage the unique know-how of my laboratory generated during the ERC funding period and establish a company that will offer biology researchers assistance with all aspects of light sheet microcopy from hardware, through operation to computational data analysis. We plan to establish an expandable light sheet microscopy service - spim4You – at a time when this powerful technique enters the research mainstream and was named Method of the Year by Nature Methods.

 Publications

year authors and title journal last update
List of publications.
2016 Christopher Schmied, Peter Steinbach, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak
An automated workflow for parallel processing of large multiview SPIM recordings
published pages: 1112-1114, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/btv706
Bioinformatics 32/7 2019-07-25
2016 Sollich, H., von Zadow, U., Pietzsch, T., Tomancak, P., Dachselt, R.
Exploring Time-dependent Scientific Data Using Spatially Aware Mobiles and Large Displays.
published pages: , ISSN: , DOI:
Proceedings of the 2016 ACM on Interactive Surfaces and Spaces (2016) 2019-07-25
2016 Johannes Girstmair, Anne Zakrzewski, François Lapraz, Mette Handberg-Thorsager, Pavel Tomancak, Peter Gabriel Pitrone, Fraser Simpson, Maximilian J. Telford
Light-sheet microscopy for everyone? Experience of building an OpenSPIM to study flatworm development
published pages: , ISSN: 1471-213X, DOI: 10.1186/s12861-016-0122-0
BMC Developmental Biology 16/1 2019-07-25
2016 Christopher Schmied, Pavel Tomancak
Sample Preparation and Mounting of Drosophila Embryos for Multiview Light Sheet Microscopy.
published pages: 189-202, ISSN: 1940-6029, DOI: 10.1007/978-1-4939-6371-3_10
Methods in molecular biology 2019-07-25
2016 Jaroslav Icha, Christopher Schmied, Jaydeep Sidhaye, Pavel Tomancak, Stephan Preibisch, Caren Norden
Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development
published pages: , ISSN: 1940-087X, DOI: 10.3791/53966
Journal of Visualized Experiments 110 2019-07-25

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The information about "SPIM4YOU" are provided by the European Opendata Portal: CORDIS opendata.

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