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spim4You

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

Total Cost €

EC-Contrib. €

Partnership

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spim4You project word cloud

Explore the words cloud of the spim4You project. It provides you a very rough idea of what is the project "spim4You" about.

software brain powerful assistance sheet cell science samples mainstream light source shifting formidable solutions cells emerged hardware anyone platform near computational plan form microscope engineering period operation benefits living named organism expandable lights few enters cancer monitor time library microscopy grant dimensional company revolutionize heavily computer environment interdisciplinary expertise data laboratories operate live animal physics laboratory visualization service leverage construct openspim hourglass proof idea spectacular biological analyze paradigm spim4 nature native biology modular spanning erc establishment technique microcopy follow tools skills foundation instance relies

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 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.	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

List of publications.
year	authors and title	journal	last update
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, FranÃ§ois 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.