May 2014 - FILM-Users - imperial.ac.uk

[FILM-Users 00506] FILM Microscopy Day 2014
by Martin Spitaler 31 May '14

31 May '14

Dear microscopists, the academic year is approaching its end, and as usual we conclude our FILM Club series with the FILM Microscopy Day 2014: *FILM MICROSCOPY DAY 2014, Wednesday 25 June, SAFB-G34 (South Kensington Campus), 10.00-17.00* Again a whole day full of exciting talks and presentations about microscopy, better and bigger than ever - this time with not one, but two plenary lectures, one by internal microscopist Cristina Lo Celso, the other by Phillip Kukura from Oxford. And we hope many of you will add to the exciting programme with your own 3-min presenation of the microscopy you are doing in your lab: The Microscopy Matchmaker Session has always been a highlight of the day, and the more presentations we get, the more fun it will be, and the better your chances of getting to know other people's work and starting new collaborations. See also the full invitation at <https://workspace.imperial.ac.uk/imagingfacility/Public/FILM%20Microscopy%2…> So keep the day free, good imaging, Martin http://www3.imperial.ac.uk/imagingfacility/news#md _*Agenda *_ *_Morning Session_*** *10.00-10.15Welcome and latest FILM News (Tony Magee) *New microscopes, new equipment, new staff *10.15-11.15 Basics of microscopy (Martin Spitaler, FILM) *Image formation, fluorescence, visualisation, quantitation */11.15-11.35 coffee & tea break/*** *11.35-12.15 Sample preparation for live and fixed samples (Stephen Rothery, FILM) *Fixatives, strategies, viability, autofluorescence ** *_Microscopy Match-Maker_*** *12.15-13.00 Microscopy Match-Maker *Research performed in FILM, presented by users through 3 min snapshot presentations */13.00-14.00 Sandwich lunch /*/with opportunity to see the new super-resolution microscope / *_Afternoon Session_*** *14.00-14.40 Super-resolution microscopy (Debora Keller, FILM) *PALM, STORM, SIM, resolution limits, artefacts */14.40-15.00 coffee & tea break/*** *_PLENARY SESSION _*** *15.00-15.55Cristina Lo Celso, Imperial College: /"Intra-vital imaging in stem cell biology"/* *15.55-16.50 Philipp Kukura, Oxford/: "Molecular Imaging"/* *16.50-17.00 Tony Magee: Round-up * ** *FILM Microscopy Day 2014: Plenary session*** *Cristina Lo Celso, Imperial College*: */"Intra-vital imaging in stem cell biology"/* After a PhD from University College London in the field of epidermal stem cell biology, Dr Lo Celso worked as a postdoc at Harvard University developing intra-vital microscopy of the haematopoietic stem cell niche. In 2009 she was appointed assistant professor at Imperial College London, where she has established a research group focussing on understanding the cellular mechanisms regulating haematopoietic stem cell (HSC) function and leukaemia development and . In close collaboration with FILM, her group has developed tools to study HSCs in their native bone marrow environment. She will present an interdisciplinary approach combining intra-vital microscopy techniques, computational image analysis, molecular profiling and mathematical modelling and the group's most recent observations of the dynamic interactions between HSCs and the bone marrow microenvironment. *Philipp Kukura, Oxford/: "Molecular Imaging" /* The primary goal of optical microscopy is to visualise microscopic structure and dynamics. Developments over the past decades have enabled routine studies down to the single molecule level and structural observations far beyond the diffraction limit through the use of fluorescence as a contrast mechanism. Despite its many advantages, one of the fundamental limitations of fluorescence detection is the frequency with which photons can be emitted and thus detected. As a consequence, imaging speeds remain limited to few to tens of frames per resulting in a considerable gap between the speed at which dynamics can be recorded and the speed of motion on the nanoscale. I will describe an alternative approach to optical microscopy that relies on the ultra-efficient detection of light scattering called interferometric scattering microscopy (iSCAT). I will show that iSCAT can follow the motion of nanoscopic labels with nm precision down to the microsecond regime, the relevant timescale for a majority of dynamics on the nanoscale. Thereby, we are able to address a surprising variety of fundamental questions ranging from the mechanism underlying processive molecular motion to the existence and formation of lipid rafts in membranes. Finally, I will show that iSCAT can detect, image and track the motion of single, proteins using light scattering without the need for any labels. _* *_ -- ------------------------------------------------------------------------ *Martin Spitaler, PhD* *FILM - Facility for Imaging by Light Microscopy* - Facility Manager - Sir Alexander Fleming Building 401 Imperial College London / South Kensington Exhibition Road London SW7 2AZ UK

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[FILM-Users 00504] looking after the microscopes
by Martin Spitaler 29 May '14

29 May '14

Dear microscopists, today unfortunately I have to remind you to be more careful and cooperative looking after FILM microscopes - some of you have become quite reckless, and this is creating lost time, bad image quality and other problems for other users: * Please be _*very*_ _*careful with the lenses*_: Someone has just damaged the 63x water immersion objective on Confocal 3, we have to send it in for repair, which will probably cost at least £1,000; if you can't find the focus, try with low magnification first, and go to the edge of your slide, dish or coverslip, which is always easy to see. * When using oil immersion objective lenses, only use a _*small drop of oil*_, and wipe the lens between samples. Recently, microscopes were regularly soaked with immersion oil (in particular on CF4), which went into the microscope body, onto all air objectives and everywhere else. This means that users get bad quality images, and staff spend a long time cleaning microscope and lenses. * The *stage insert for multiwell plates *for Leica confocals had disappeared and was urgently needed for a project; we had to order a replacement, and suddenly it has reappeared - another £450 wasted. * _*Rubbish:*_ Please clean the microscope space after yourself, put all rubbish in the appropriate bin: Lab waste into clinical waste bins, everything else into the normal bins - do _*not*_ through any coffee cups or similar into the clinical waste bins, it costs a lot of money to have them incinerated! * If you spill liquid or break glass, please also clean it up! It's not acceptable if the next microscope user has to spend the first part of the session to clean the space (as happened recently on CF3 with broken glass). If things go wrong and you don't know how best to clean it, please ask. I hope this will help to remind the few people behaving badly what effect their negligence has and do better in the future. Thanks for your cooperation, good imaging, Martin -- ------------------------------------------------------------------------ *Martin Spitaler, PhD* *FILM - Facility for Imaging by Light Microscopy* - Facility Manager - Sir Alexander Fleming Building, desk 401 Imperial College London / South Kensington Exhibition Road London SW7 2AZ UK Tel. +44-(0)20-759-42023 E-mail m.spitaler(a)imperial.ac.uk <mailto:m.spitaler@imperial.ac.uk> Website: http://imperial.ac.uk/imagingfacility

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[FILM-Users 00503] new ONIX perfusion system available in FILM
by Martin Spitaler 28 May '14

28 May '14

Dear microscopists, thanks to a grant application organised mainly by Brian Robertson, we have now a new perfusion system available in FILM, the CellAsic ONIX microfluidic platform: * http://www.cellasic.com/ONIX.html * http://www.millipore.com/life_sciences/flx4/cellasic_live_cell_imaging#tab1… (the system was recently bought by Millipore) Currently, the system is implemented on Widefield 2, but the perfusion plates are the size of a multiwell plate, so in principle fits on any inverted microscope (the software needs to be installed). Plates are available for bacteria, yeast and mammalian cells, but after the take-over by Millipore a new round of standardisation and upscaling has resulted in temporary shortages for some of the plates. Application notes and descriptions - including some impressive videos - are available on the website and also on the FILM Documentation Server (\\film-nas.med.ic.ac.uk\documentation) in the folder "...\Cellasic\". The system is already pretty busy, but if you are interested, please get in touch with FILM staff. Good imaging, Martin -- ------------------------------------------------------------------------ *Martin Spitaler, PhD* *FILM - Facility for Imaging by Light Microscopy* - Facility Manager - Sir Alexander Fleming Building, desk 401 Imperial College London / South Kensington Exhibition Road London SW7 2AZ UK Tel. +44-(0)20-759-42023 E-mail m.spitaler(a)imperial.ac.uk <mailto:m.spitaler@imperial.ac.uk> Website: http://imperial.ac.uk/imagingfacility

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[FILM-Users 00502] new FILM data servers
by Martin Spitaler 20 May '14

20 May '14

Dear microscopists, after long planning and hard work by the Bioinformatics Support Service (BSS) testing everything to make the transition smooth, we are finally in a position to move over to the new data servers purchased with support from the college's Equipment Sharing grant: OMERO, Definiens, Huygens deconvolution and in the future other software will profit from much more powerful processing and data storage capacity. The plan is to move everything over this coming Friday 23 May in the morning. If everything goes smoothly, they might be up and running again at lunch time, but expect interruptions the whole day, just to prepare for the worst. Two questions to you users: First, is it ok if these tools are unavailable this Friday for a few hours? And second, very importantly: To speed up the process and avoid wasting resources, could you please *delete all old data* *from the Definiens / Huygens servers*? Good imaging, Martin -- ------------------------------------------------------------------------ *Martin Spitaler, PhD* *FILM - Facility for Imaging by Light Microscopy* - Facility Manager - Sir Alexander Fleming Building, desk 401 Imperial College London / South Kensington Exhibition Road London SW7 2AZ UK Tel. +44-(0)20-759-42023 E-mail m.spitaler(a)imperial.ac.uk <mailto:m.spitaler@imperial.ac.uk> Website: http://imperial.ac.uk/imagingfacility

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[FILM-Users 00501] Fwd: OMERO Viewer / BBSRC Grant
by Martin Spitaler 01 May '14

01 May '14

Dear all, I'm forwarding this request from Stephen Taylor for people interested in the development of his tool to view and sort large numbers of images in an efficient way, who would be willing to cooperate on his grant application. It's a short deadline, so if you are interested please get in touch soon. Best regards, Martin -------- Original Message -------- Subject: OMERO Viewer / BBSRC Grant Date: Wed, 30 Apr 2014 16:21:29 +0000 From: Stephen Taylor <stephen.taylor(a)imm.ox.ac.uk> To: m.spitaler(a)imperial.ac.uk <m.spitaler(a)imperial.ac.uk> CC: Ian Dobbie <ian.dobbie(a)bioch.ox.ac.uk> Dear Martin, I was discussing with Ian Dobbie in Oxford about groups in the UK that are using OMERO and he mentioned your name so I hope you don't mind me emailing you. I am writing a grant to the BBSRC to interface our PivotViewer application (the new version we are calling Zegami) which allows querying and visualisation of thousands of images in which we plan to interface with OMERO. The abstract to this is attached. The best introduction is probably the following YouTube video which demos it in use. * YouTube introductory video: https://www.youtube.com/watch?v=BvDOPpRo7KM Jason Swedlow, is supporting the bid and I was wondering if you could see a demand for this at your facility? Happy to discuss via email or on the phone if you have time. Kind regards and thanks, Steve ======================================= Head of Computational Biology Research Group Weatherall Institute of Molecular Medicine University of Oxford +44 1865 222640 www.cbrg.ox.ac.uk

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