September 2013 - FILM-Users

[FILM-Users 00347] Definiens training course
by Martin Spitaler 30 Sep '13

30 Sep '13

Dear microscopists, I'm very pleased to let you know that we have recently been successful with an application for the College's "equipment sharing grant", and part of of the money will pay towards two training courses for the powerful Definiens Developer XD software, one for beginners and one for advanced users. This will mean that both training courses will be available at a subsidised rate of probably ~£200-300 per participants (rates still need to be finalised, also dependent on the number of participants). Many of you have already used the Definiens software for a range of challenging image analysis tasks, from finding vesicles in noisy confocal images to identifying cells in 3D datasets, multi-parameter analysis of muscle fibres to immunological synapses. The power of the software lies in the easy access to a large range of professional image analysis and computer vision tools - with full control of all parameters - and in a dedicated architecture for large-scale batch processing (the largest dataset so far consisted of >30,000 images). It also contains tools for cell tracking, fuzzy logics and machine learning, which might be covered in the advanced course - this will depend on user demand. Please let me know if you are interested in attending either of the two training courses. And if you are not sure - if there is enough interest to learn more about the software, we could use the May FILM Club (31st of May) to give you an overview, based on projects in FILM. Good imaging, Martin PS: other improvements covered by the Equipment Sharing Grant are upgrades to our Widefield 2 microscope (64bit computer to deal with larger data files for live imaging, RGB camera for histological sections) and a new data processing server, which will allow processing of much larger datasets -- ------------------------------------------------------------------------ *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 00410] Fwd: Multidimensional fluorescence imaging workshop
by Martin Spitaler 25 Sep '13

25 Sep '13

...forwarded for your information, Martin -------- Original Message -------- Subject: Multidimensional fluorescence imaging workshop Date: Wed, 25 Sep 2013 13:32:56 +0100 From: French, Paul (PHOT) M W (Photonics) <paul.french(a)imperial.ac.uk> *Multidimensional fluorescence imaging and metrology* Photonics Group user workshop for cell biology, HCA and clinical diagnosis Friday September 27, 2013, Lecture Theatre 2, Physics Department, Imperial College London, SW7 2AZ 0930 Coffee Posters (Blackett, Foyers Level 2 & 3) 1000 Paul French Welcome and introduction to multidimensional fluorescence imaging and metrology research portfolio 1030 Poster presenters Poster preview talks 1055 Mark Neil Super-resolved microscopy and optogenetics 1115 Poster presenters Poster preview talks 1140 Sean Warren & Yuriy Alexandrov Data analysis and management: FLIMfit and OMERO 1155 Poster presenters Poster preview talks 1220 Lunch Posters (Blackett, Foyers Level 2 & 3) 1345 David Spiller (Manchester) High Content Time lapse Microscopy for Systems Biology 1415 Robert Mahen (EMBL) Generation of functional fluorescently tagged transgenes in human cells for systems microscopy 1435 Chris Dunsby High speed 2D and 3D fluorescence imaging by oblique plane microscopy 1455 James McGinty FLIM tomography of live disease models: zebrafish and mice 1515 Tea Posters (Blackett, Foyers Level 2 & 3) 1545 Erik Sahai (LRI-CRUK) Intravital Imaging of Cancer Signalling and Response to Therapy Using FRET Biosensors 1615 Sergio Coda Clinical fluorescence lifetime metrology for GI cancer 1630 Rakesh Patalay Clinical multispectral multiphoton FLIM microscopy of skin disease 1645 Discussion Future trend and priorities 1700 Maggie Dallman Closing remarks Drinks & canapés Posters (Blackett, Foyers Level 2 & 3) Posters Advances in microscopy Hugo Sinclair 3-D STED microscopy and its application to imaging luminescent defects in diamond Alex Savell Application of STED microscopy to image the immunological synapse Lionel Fafchamps Development of high speed optical sectioning microscopes based on structured illumination Lionel Chaudet Development of highly parallel optical systems for optogenetics FLIM and FRET of cell signalling George Chennell Development and application of FRET biosensors to probe metabolic changes in live cells and spheroid cultures Sean Warren Multiplexed FRET of cell signalling during chemotaxis Dominic Alibhai Automated FLIM FRET assay of HIV Gag protein oligomerisation Doug Kelly Automated plate reading FLIM microscope and applications to cell-based FRET assays for protein-protein interactions Doug Kelly Automated plate reading FLIM microscope: live cell autofluorescence lifetime assays Mesoscopic to macroscopic fluorescence tomography Vincent Maioli Applications of oblique plane microscopy to the study of calcium sparks in isolated cardiac myocytes Yuriy Alexandrov Automated MDFI analysis for cell-based assays and clinical diagnosis Sunil Kumar Rapid OPT for longitudinal studies of cancer and inflammation in live adult zebrafish Lingling Chen Advances in optical projection tomography Natalie Andrews FLIM and FRET in live zebrafish Clinical multidimensional fluorescence imaging and metrology Hugh Sparks FLIM endoscopy Joao Lagarto Compact multispectral autofluorescence lifetime fiber-optic probes Ben Dyer Ex vivo and in vivo application of fluorescence lifetime metrology to heart disease Mohammad Nickdel Application of autofluorescence lifetime metrology to label-free diagnosis of osteoarthritis Refreshments courtesy of Andor Technology and Photometrics & QImaging

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[FILM-Users 00409] TODAY Fwd: RE: Outstanding lecture from Mark Ellisman on 24 September, 1600 Read Lecture Theatre, Level 5, Sherfield Building
by Martin Spitaler 24 Sep '13

24 Sep '13

_*Tuesday, September 24, 2013 -- 16:00 h*_ Venue: Read Lecture Theatre, Level 5, Sherfield Building, South Kensington Campus, Imperial College London *Leica Scientific Forum UK -- London** * _*Advances in Life Science Prof. Mark Ellisman Director of NCMIR and CRBS, University of California San Diego*__* *__*"Multiscale Microscopy of the Brain: Where is the Dark Matter?"*__* *_ Lecture This talk will highlight projects in which development and application of new contrasting methods and imaging tools have allowed us to observe otherwise hidden relationships be- tween cellular, subcellular and molecular constituents of cells, including those of nervous systems. Prof. Ellisman will present * New chemistries for carrying out correlated light and electron microscopy * Recent advances in large-scale high-resolution 3D reconstruction with LM, TEM and SEM based methods. * Next generation cell-centric image libraries and web-based multiscale information ex- ploration environments for sharing and exploring these data 16:00 Welcome & Introduction by Prof. Keith Willison 17:30 Discussion and post lecture reception Scientific Advisory Board UK: Prof. Keith Willison, Prof. Paul French (Imperial College London), Prof. Tony Ng (King's College London), Prof. Antony Galione, Prof. Gero Miesenboeck, Prof. Tony Wilson (Oxford Univ.), Prof. David Klenerman, Dr. Jim Haseloff (Cambridge Univ.), and Dr. Thomas Zapf (Leica Microsystems) The lecture is free. Please kindly register: lsf(a)leica-microsystems.com Learn more: www.leica-microsystems.com/events/leica-scientific-forum/

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[FILM-Users 00407] Fwd: ome-users Digest, Vol 102, Issue 12
by Martin Spitaler 18 Sep '13

18 Sep '13

...forwarded for your information; I saw Douglas' presentation at the OMERO meeting in June, and this is really a promising tool, worth trying, Martin -------- Original Message -------- Subject: ome-users Digest, Vol 102, Issue 12 Date: Wed, 18 Sep 2013 12:00:01 +0100 From: <ome-users-request(a)lists.openmicroscopy.org.uk> Reply-To: <ome-users(a)lists.openmicroscopy.org.uk> To: <ome-users(a)lists.openmicroscopy.org.uk> Send ome-users mailing list submissions to ome-users(a)lists.openmicroscopy.org.uk To subscribe or unsubscribe via the World Wide Web, visit http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users or, via email, send a message with subject or body 'help' to ome-users-request(a)lists.openmicroscopy.org.uk You can reach the person managing the list at ome-users-owner(a)lists.openmicroscopy.org.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of ome-users digest..." Today's Topics: 1. OMERO.webtagging beta release (Helen Flynn) ---------------------------------------------------------------------- Message: 1 Date: Tue, 17 Sep 2013 16:33:38 +0000 From: Helen Flynn <h.flynn(a)dundee.ac.uk> To: "<ome-users(a)lists.openmicroscopy.org.uk>" <ome-users(a)lists.openmicroscopy.org.uk>, "<ome-devel(a)lists.openmicroscopy.org.uk>" <ome-devel(a)lists.openmicroscopy.org.uk> Subject: [ome-users] OMERO.webtagging beta release Message-ID: <DDA1D23E-F0F2-4D35-B533-07918559F135(a)dundee.ac.uk> Content-Type: text/plain; charset="us-ascii" Dear All, The OME consortium are pleased to announce the beta release of the OMERO.webtagging auto-tagging tool developed by Douglas Russell, an OME developer based at Oxford University. See http://www.openmicroscopy.org/site/products/partner/omero.webtagging/ for further details. Douglas has previously talked at the OME User Meetings[1] and other venues on the benefits of using OMERO Tagging as a way of replacing hierarchies, which are used heavily when organizing data on the file system. This is the first (released) step to achieving that goal. As described in the documentation[2], Douglas is keen to hear from anyone who has problems, suggestions or feedback as the tool is still under development, and as always, you are welcome to start a discussion on this mailing list. Regards, The OME Team [1]http://www.openmicroscopy.org/site/community/minutes/meetings/june-2013-p… [2] http://www.openmicroscopy.org/site/support/partner/omero.webtagging The University of Dundee is a registered Scottish Charity, No: SC015096 ------------------------------ _______________________________________________ ome-users mailing list ome-users(a)lists.openmicroscopy.org.uk http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users End of ome-users Digest, Vol 102, Issue 12 ******************************************

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[FILM-Users 00408] Fwd: Post-doctoral positions available in optical imaging, biosensors and physiology
by Martin Spitaler 18 Sep '13

18 Sep '13

...forwarded for your information, Martin -------- Original Message -------- Subject: Post-doctoral positions available in optical imaging, biosensors and physiology Date: Tue, 17 Sep 2013 17:13:10 +0200 From: Daniel Choquet <daniel.choquet(a)u-bordeaux2.fr> To: <m.spitaler(a)imperial.ac.uk> Dear Dr. Spitaler, I'm seeking your help in identifying outstanding pots-doctoral candidates to join my research group in the coming year. I thank you in advance for posting this add (attached) in your department. With my best regards Daniel Post-doctoral positions are available starting fall 2013-spring 2014 at the Institute for Interdisciplinary Neuroscience in the group "dynamic organization of synapses", headed by Daniel Choquet and funded by grants from the European Research Council (ERC) and the Ministry of research (ANR) to work in an interdisciplinary environment on the molecular and cellular mechanisms of synapse organization and plasticity, in particular combining super-resolution technique and electrophysiology on cell cultures and brain slices. (See Heine et al. Science 2008, Opazo et al, Neuron 2010, Nair et al. J. Neuro 2013). Candidates less than four years after their PhD with excellent past-record of achievement will have expertise in one of the following: cell biology, high resolution or single molecule imaging, brain slice electrophysiology. Projects range from the analysis of AMPA receptor organization and trafficking at the single molecule level and their physiological function to the development of new high resolution imaging methods and bio-sensors. For application, informal information or pre-application discussions may be conducted via e-mail. Application should include a letter of motivation, a CV and a short summary of your current researches and center of scientific interest. More details in: http://www.iins.u-bordeaux2.fr/research-teams/daniel-choquet-team http://www.bic.u-bordeaux2.fr/ Contact: Please send CV and two letters of recommendation to: IINSrecruit(a)gmail.com <mailto:IINSrecruit@gmail.com> Daniel Choquet, Interdisciplinary Institute for Neuroscience, IINS, CNRS UMR 5297 146 rue Léo Saignat 33077 Bordeaux Cedex, France IINS, UMR 5297 CNRS-Université Bordeaux Segalen Institut Interdisciplinaire de NeuroScience BIC, UMS 3420 CNRS-US 004 INSERM-Université Bordeaux Segalen Bordeaux Imaging Center 146 rue Léo Saignat 33077 Bordeaux Cédex Tel 33 (0) 5 57 57 40 90 Fax 33 (0) 5 57 57 40 82 email dchoquet(a)u-bordeaux2.fr <mailto:dchoquet@u-bordeaux2.fr> IINS web site:http://www.iins.u-bordeaux2.fr/ Bordeaux Imaging Center :http://www.bic.u-bordeaux2.fr/

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[FILM-Users 00406] Fwd: RE: Outstanding lecture from Mark Ellisman on 24 September, 1600 Read Lecture Theatre, Level 5, Sherfield Building
by Martin Spitaler 17 Sep '13

17 Sep '13

...forwarded for your information - don't miss it, unlike other some talks of this series more aimed at hard-core microscopists, this one should be interesting for everyone from molecular biology to fans of Hollywood movies.... come along and see, Martin Tuesday, September 24, 2013 -- 16:00 h Venue: Read Lecture Theatre, Level 5, Sherfield Building, South Kensington Campus, Imperial College London *Leica Scientific Forum UK -- London** * _*Advances in Life Science Prof. Mark Ellisman Director of NCMIR and CRBS, University of California San Diego*__* *__*"Multiscale Microscopy of the Brain: Where is the Dark Matter?"*__* *_ Lecture This talk will highlight projects in which development and application of new contrasting methods and imaging tools have allowed us to observe otherwise hidden relationships be- tween cellular, subcellular and molecular constituents of cells, including those of nervous systems. Prof. Ellisman will present * New chemistries for carrying out correlated light and electron microscopy * Recent advances in large-scale high-resolution 3D reconstruction with LM, TEM and SEM based methods. * Next generation cell-centric image libraries and web-based multiscale information ex- ploration environments for sharing and exploring these data 16:00 Welcome & Introduction by Prof. Keith Willison 17:30 Discussion and post lecture reception Scientific Advisory Board UK: Prof. Keith Willison, Prof. Paul French (Imperial College London), Prof. Tony Ng (King's College London), Prof. Antony Galione, Prof. Gero Miesenboeck, Prof. Tony Wilson (Oxford Univ.), Prof. David Klenerman, Dr. Jim Haseloff (Cambridge Univ.), and Dr. Thomas Zapf (Leica Microsystems) The lecture is free. Please kindly register: lsf(a)leica-microsystems.com Learn more: www.leica-microsystems.com/events/leica-scientific-forum/

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[FILM-Users 00405] PA-mCherry
by Xu, Huifang 17 Sep '13

17 Sep '13

Dear All, I am looking for cDNA for PA-mCherry (photoactivatable mCherry) to fuse to our protein for super-resolution microscopy. Does anyone here use it or know someone who uses it? Thanks very much! Kind regards, Huifang

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[FILM-Users 00404] FILM server full
by Martin Spitaler 16 Sep '13

16 Sep '13

Dear microscopists, the scratch disk on the FILM server is filling up again, to avoid problems for users with large datasets moving them around we need to delete data. Please don't forget that this is a TEMPORARY space to move data around, NOT to store them. Make sure you have your data save somewhere else, as they can disappear at any time without notice, whenever space is required. As a more reliable solution, we recommend using the space provided by BSS as part of the OMERO setup, which is what we also use in the facility. This way, our data are not only save and double-backed up, but we can also find them again later, thanks to easy visualisation and annotation. 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 00403] FLIM-Fit software
by Martin Spitaler 13 Sep '13

13 Sep '13

...forwarded for your information - and congratulations Sean and Ian, Martin -------- Original Message -------- Subject: ome-users Digest, Vol 102, Issue 6 Date: Mon, 9 Sep 2013 12:00:01 +0100 From: <ome-users-request(a)lists.openmicroscopy.org.uk> Reply-To: <ome-users(a)lists.openmicroscopy.org.uk> To: <ome-users(a)lists.openmicroscopy.org.uk> To subscribe or unsubscribe via the World Wide Web, visit http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users or, via email, send a message with subject or body 'help' to ome-users-request(a)lists.openmicroscopy.org.uk Dear All, The OME consortium is pleased to announce that FLIMfit, an OMERO client for FLIM data developed by the Photonics Group at Imperial College London, has been published in PLOS ONE - http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0070687 The software is available to download from http://www.openmicroscopy.org/site/products/partner/flimfit/downloads Regards, The OME team Dr Helen Flynn OME Technical Writer Centre for Gene Regulation & Expression Open Microscopy Environment University of Dundee http://openmicroscopy.org<http://openmicroscopy.org/> The University of Dundee is a registered Scottish Charity, No: SC015096

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