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Persistent URL http://purl.org/net/epubs/work/63672
Record Status Checked
Record Id 63672
Title Single molecule microscopy IT infrastructure for the OCTOPUS cluster
Contributors
Abstract The OCTOPUS imaging cluster in the Lasers for Science Facility in STFC provides a range of fluorescence imaging techniques including multidimensional single molecule microscopy, confocal microscopy, and optical profilometry, and is used to solve problems in the life sciences, particularly in areas where understanding molecular interactions is crucial. Significant effort has been invested in recent years in developing the software side of this facility, focussing in particular on single molecule microscopy data acquisition and automated analysis, where flexible solutions to handle a growing variety of different experimental configurations and methods are needed. Developments include custom data acquisition software using Labview and an advanced Bayesian multidimensional single molecule feature detection, tracking and visualisation pipeline using C++, GTK and Cairo [1]. Work is now also underway to improve the infrastructure for management of data and computational resources and the experience of external users. This will enable more effective scaling of resources to cope with increasing demands, and includes data management using ICAT, job management using Torque and remote access for users to both the data and the analysis and visualisation facilities through a custom web portal. We discuss our chosen methods and technologies, the difficulties encountered and future plans and challenges. References 1. Clarke D.T., Botchway S.W., Coles B.C., Needham S.R., Roberts S.K., Rolfe D.J., Tynan C.J., Ward A.D., Webb S.E.D., Yadav R., Zanetti-Domingues L., Martin-Fernandez M.L., Optics clustered to output unique solutions: A multi-laser facility for combined single molecule and ensemble, Rev. Sci. Inst, 82, Article Number: 093705 (2011). 2. Rolfe D.J., McLachlan C.I., Hirsch M., Needham S.R., Webb S.E.D., Martin-Fernandez M.L., Hobson M.P., Automated multidimensional single molecule fluorescence microscopy feature detection and tracking, Eur Biophys J, 40, 1167-1186 (2011).
Organisation CLF , STFC
Keywords NOBUGS2012
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Language English (EN)
Type Details URI(s) Local file(s) Year
Presentation Presented at NOBUGS 2012 (NOBUGS 2012), Rutherford Appleton Laboratory, Didcot, England, 24-26 Sept 2012. MHirsch_nobugs12.ppt
supplementary movie 2.avi
20080411_0002_0004_track298.avi		 2012