- FILM-Users - imperial.ac.uk

[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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[FILM-Users 00500] CANCELLED: FILM Club - Amanda Wilson: "The Histocutter: A revolution in 3D imaging"
by Martin Spitaler 30 Apr '14

30 Apr '14

Dear microscopists, very unfortunately it turns out that as an indirect effect of the tube strike, we have to cancel today's FILM Club - Amanda tried to cycle in yesterday despite a back strain, which made it much worse. On this occasion, watch out for the FILM MICROSCOPY DAY coming up in two months' time, on Wednesday the 25th of June. Again full of interesting presentations with a plenary speaker (tbc) at the end. Good imaging, Martin -------- Original Message -------- Subject: FILM Club TODAY - Amanda Wilson: "The Histocutter: A revolution in 3D imaging" Date: Wed, 30 Apr 2014 10:24:39 +0100 From: Martin Spitaler <m.spitaler(a)imperial.ac.uk> To: FILM-Users mailing list <film-users(a)imperial.ac.uk> Dear microscopists, TODAY is FILM Club day again, with yet another rather unusual talk, very interesting: *Amanda Wilson: "The Histocutter: A revolution in 3D imaging"* *Wednesday 30th of April 2014, 4.30pm, SAFB-122 (South Kensington Campus)** * Many studies can benefit from 3D microscopy, with its ability to resolve complex features or structural relationships within a volume. However, certain types of samples, such as hard tissues and whole eyes, are too large or optically dense to image with a confocal microscope. In the past, the only alternative was to conduct time-consuming serial section collection and reconstruction, or to settle for 2D microscope imaging and analysis. The Histocutter was specifically designed to address this imaging niche, by employing an automated cut-and-view approach that circumvents traditional optical limitations. Recently improved and perfected here in the Department of Bioengineering, this robotic device can perform high-throughput, high resolution, 3d histological imaging. Thousands of multi-spectral high quality images can be automatically captured and aligned, ready for quantitative analysis and 3D-visualisation. Orthogonal resolutions can approach 1um, whilst sample sizes can be relatively large (maximum 900 x 1500um), and in this respect, the Histocutter is truly unique. The Histocutter is particularly well suited to small animal studies, especially samples where the optical penetration is limited, for example bone and cartilage, and whole mouse eyes. Vascular tracers, bone growth indicators (calcein, alizarin red) and en-bloc dyes can be imaged, and unstained tissue can also be processed. Typical samples include whole organs from small animals (e.g. brain, bone, heart), engineered scaffolds seeded with cells, tissue explants and patient biopsies, including cancer biopsies, and whole lymph nodes. Other applications include the validation of Micro-CT data and integration into correlative studies. This lecture will highlight several recent research projects in which the Histocutter has played a key role, showcasing the great images that can be obtained using this system, and promoting the system as a valuable departmental resource. Contributions to Osteoarthritis, Glaucoma, Neurotechnology and Blast Centre research will be disseminated, as well as key aspects of project design, sample preparation and 3D visualization and analysis. See you there, 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 00499] FILM Club TODAY - Amanda Wilson: "The Histocutter: A revolution in 3D imaging"
by Martin Spitaler 30 Apr '14

30 Apr '14

Dear microscopists, TODAY is FILM Club day again, with yet another rather unusual talk, very interesting: *Amanda Wilson: "The Histocutter: A revolution in 3D imaging"* *Wednesday 30th of April 2014, 4.30pm, SAFB-122 (South Kensington Campus)** * Many studies can benefit from 3D microscopy, with its ability to resolve complex features or structural relationships within a volume. However, certain types of samples, such as hard tissues and whole eyes, are too large or optically dense to image with a confocal microscope. In the past, the only alternative was to conduct time-consuming serial section collection and reconstruction, or to settle for 2D microscope imaging and analysis. The Histocutter was specifically designed to address this imaging niche, by employing an automated cut-and-view approach that circumvents traditional optical limitations. Recently improved and perfected here in the Department of Bioengineering, this robotic device can perform high-throughput, high resolution, 3d histological imaging. Thousands of multi-spectral high quality images can be automatically captured and aligned, ready for quantitative analysis and 3D-visualisation. Orthogonal resolutions can approach 1um, whilst sample sizes can be relatively large (maximum 900 x 1500um), and in this respect, the Histocutter is truly unique. The Histocutter is particularly well suited to small animal studies, especially samples where the optical penetration is limited, for example bone and cartilage, and whole mouse eyes. Vascular tracers, bone growth indicators (calcein, alizarin red) and en-bloc dyes can be imaged, and unstained tissue can also be processed. Typical samples include whole organs from small animals (e.g. brain, bone, heart), engineered scaffolds seeded with cells, tissue explants and patient biopsies, including cancer biopsies, and whole lymph nodes. Other applications include the validation of Micro-CT data and integration into correlative studies. This lecture will highlight several recent research projects in which the Histocutter has played a key role, showcasing the great images that can be obtained using this system, and promoting the system as a valuable departmental resource. Contributions to Osteoarthritis, Glaucoma, Neurotechnology and Blast Centre research will be disseminated, as well as key aspects of project design, sample preparation and 3D visualization and analysis. See you there, 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 00498] COMMERCIAL Fwd: DRAQ7 starter pack launch
by Martin Spitaler 29 Apr '14

29 Apr '14

....COMMERCIAL Fwd... -------- Original Message -------- Subject: DRAQ7 starter pack launch Date: Tue, 29 Apr 2014 05:17:22 -0700 From: Stefan Ogrodzinski <enquiry(a)biostatus.com> Reply-To: enquiry(a)biostatus.com <campaigns.676603.22433.d22b54bb36(a)campaigns.netsuite.com> To: <m.spitaler(a)imperial.ac.uk> Hi Folks! We are always excited when we launch a new product at BioStatus, so I hope you don't mind me alerting you at the earliest opportunity. This month we are introducing a *new DRAQ7™ starter pack*, code: *DR70250* priced at just *GBP£75* DRAQ7™ is probably the best viability dye on the market! It has been described in a wide range of cell types (>30 cell types so far) to report cell death and apoptosis. It's far-red fluorescent signature works great in combination with a whole range of fluors including the Brilliant Violet dyes, allowing you to squeeze the very most out of your flow cytometer. You can read much more about DRAQ7™ at our website - http://www.biostatus.com/DRAQ7_s/1836.htm - where you will find links to lots of useful information and of course you can always contact us directly - enquiry(a)biostatus.com - with any burning questions! We look forward to hearing from you soon! Sincerely yours Stefan *Stefan Ogrodzinski Director/CEO* e: enquiry(a)biostatus.com *BioStatus - the home of DRAQ5™ and DRAQ7™* ------------------------------------------------------------------------ You are subscribed as <m.spitaler(a)imperial.ac.uk>. Click here <http://marketing.biostatus.com/app/crm/marketing/campaignlistener.nl?__lstr…> to manage your email subscription preferences. Click here <http://marketing.biostatus.com/app/crm/marketing/campaignlistener.nl?__lstr…> or reply to this email with 'unsubscribe' in the subject to unsubscribe from this list or if you feel you have received this message in error. This message was sent from BioStatus Limited, VAT Registration Number: GB 755 5893 80 BioStatus 56A Charnwood Road Shepshed Leics. LE12 9NP United Kingdom (GB). Click here <http://marketing.biostatus.com/app/site/crm/externalcasepage.nl?compid=NLCO…> to report email abuse.

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[FILM-Users 00497] FILM Club this Wednesday - Amanda Wilson: "The Histocutter: A revolution in 3D imaging"
by Martin Spitaler 28 Apr '14

28 Apr '14

Dear microscopists, this week is FILM Club week again, with yet another rather unusual talk, very interesting: *Amanda Wilson: "The Histocutter: A revolution in 3D imaging"* *Wednesday 30th of April 2014, 4.30pm, SAFB-122 (South Kensington Campus)** * Many studies can benefit from 3D microscopy, with its ability to resolve complex features or structural relationships within a volume. However, certain types of samples, such as hard tissues and whole eyes, are too large or optically dense to image with a confocal microscope. In the past, the only alternative was to conduct time-consuming serial section collection and reconstruction, or to settle for 2D microscope imaging and analysis. The Histocutter was specifically designed to address this imaging niche, by employing an automated cut-and-view approach that circumvents traditional optical limitations. Recently improved and perfected here in the Department of Bioengineering, this robotic device can perform high-throughput, high resolution, 3d histological imaging. Thousands of multi-spectral high quality images can be automatically captured and aligned, ready for quantitative analysis and 3D-visualisation. Orthogonal resolutions can approach 1um, whilst sample sizes can be relatively large (maximum 900 x 1500um), and in this respect, the Histocutter is truly unique. The Histocutter is particularly well suited to small animal studies, especially samples where the optical penetration is limited, for example bone and cartilage, and whole mouse eyes. Vascular tracers, bone growth indicators (calcein, alizarin red) and en-bloc dyes can be imaged, and unstained tissue can also be processed. Typical samples include whole organs from small animals (e.g. brain, bone, heart), engineered scaffolds seeded with cells, tissue explants and patient biopsies, including cancer biopsies, and whole lymph nodes. Other applications include the validation of Micro-CT data and integration into correlative studies. This lecture will highlight several recent research projects in which the Histocutter has played a key role, showcasing the great images that can be obtained using this system, and promoting the system as a valuable departmental resource. Contributions to Osteoarthritis, Glaucoma, Neurotechnology and Blast Centre research will be disseminated, as well as key aspects of project design, sample preparation and 3D visualization and analysis. See you there, 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 00496] Fwd: 2014 Nikon Small World Competition
by Martin Spitaler 15 Apr '14

15 Apr '14

...forwarded for your information, Martin -------- Original Message -------- Subject: 2014 Nikon Small World Competition Date: Mon, 14 Apr 2014 16:57:53 -0400 From: David Hahn <dhahn(a)magnet.fsu.edu> To: <m.spitaler(a)imperial.ac.uk> Dear Dr. Spitaler, I hope you will be able to enter the 2014 Nikon Small World competition this year and perhaps even the new video competition: Small World in Motion. Contestants can enter up to 3 images or videos in each competition. If you are too busy or haven't had the opportunity to gather new images, let me know and I can transfer several of your previously entered images into this year's competition. Each year the competition has several hundred high-quality images that are not selected by the judges and I would like to give these images a second chance with a new set of judges. Over the past several years, many of the images that have been re-entered have gone on to win prizes. The Small World competition URL is: http://www.microscopyu.com/smallworld/scripts/entryPage1.asp The Small World Video competition URL is: http://www.microscopyu.com/smallworld/videoregistration/entrypage1.aspx Note that everyone entering the Small World 2014 competition will receive a complimentary 2015 Small World calendar. David Hahn National High Magnetic Field Laboratory 1800 East Paul Dirac Drive Florida State University Tallahassee, Florida 32310 Email: dhahn(a)magnet.fsu.edu Web: http://micro.magnet.fsu.edu

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[FILM-Users 00495] freebies
by Martin Spitaler 09 Apr '14

09 Apr '14

Dear microscopists, we have a few freebies to give away: First, a Wacom Graphire 3 graphic tablet, left behind from the Dan Davis lab; really useful for manual / interactive image analysis. Second, some FILM Image Of The Year calendars. Not all people have picked theirs up, so if you want one, come along to my desk. They are really beautiful, and the year has still 9 months to go. 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 00494] Fwd: Dan Davis lecture at the Nature headquarter: "The immune genes that make us who we are"
by Martin Spitaler 09 Apr '14

09 Apr '14

...forwarded for your information... should be really interesting; for those new(er) to Imperial College: Dan Davis was co-founder of FILM eight years ago and one of the main users, doing some spectacular cellular imaging; but this presentation is more about general immunology (and I'm sure you'll be able to buy his recent book), Martin /Nature Reviews Immunology/ presents: *a FREE Public lecture to celebrate the International Day of Immunology 2014* *The immune genes that make us who we are* *Professor Daniel M. Davis* *Tuesday, 29 April 2014, 19.00 - 21.00 The Stables Lecture Theatre, The Macmillan Building 4 Crinan Street, London, UK N1 9XW* * * Our immune system is vital for protecting us from disease-causing microorganisms, such as viruses and bacteria. Each of us has a unique set of immune genes that we use to fight these infections - our 'compatibility genes'. Not only do these genes influence whether we die or survive in the face of a particularly nasty infection, fascinating -although controversial - research suggests that they may affect the way our brains are wired, and even our choice of partner. To celebrate the International Day of Immunology, Dan Davis will tell the story of the compatibility genes of the immune system. He will discuss the Nobel Prize-winning discoveries that helped define how these genes shape immune and other biological responses, before turning to that all-important question of whether our immune genes can guide Cupid's arrows. Dan Davis is director of research at the University of Manchester's Collaborative Centre for Inflammation Research and a visiting professor at Imperial College, London. He is the author of 'The Compatibility Gene' and has published over 100 academic articles, including papers in Nature and Science, and Scientific American. The lecture will be followed by a drinks reception, 20.00-21.00. This event is *FREE* to attend and open to the general public. Click here <https://www.eventsforce.net/nature/frontend/reg/registerNew.csp?eventID=94> to reserve your place (space limited to 100 attendees) Website: https://www.eventsforce.net/nature/frontend/reg/thome.csp?pageID=34934&even… Powered by Eventsforce <http://www.eventsforce.com/home.html>

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[FILM-Users 00493] CF1 end of service
by Martin Spitaler 04 Apr '14

04 Apr '14

Dear microscopists, from next week our old and trusted *Confocal 1, the Leica SP2*, will *end its of service* for FILM. It's been used for some spectacular research - Leo Carlin, now group leader here, started a successful academic career around live imaging on it (and it produced the first Image Of The Year winner, with Angelos Skodras) - but now it needs to make space for the new super-resolution microscope. The new super-resolution microscope is still being constructed. A SIM-only version should be available from late April, the full version from mid-May. It will take some time to get everything fully tested, up and running, but then it will be available for FILM users, with support from our specialised FILM crew member Debora Keller. If you are interested, feel free to get in touch. But before you do so, make sure you have made full use of the existing microscopes available and push them to the (resolution) limits. Super-resolution microscopy is very powerful, but it has to start with the best possible samples and the best-possible normal-resolution images. 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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