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

[FILM-Users 00434] FILM application for Wellcome Trust Multi-User Equipment grant
by Martin Spitaler 31 Mar '14

31 Mar '14

Dear microscopists, following feedback from FILM users and Wellcome Trust grant holders (see summary at the bottom), the FILM steering committee has decided to use the open call for Wellcome Trust Multi-User Equipment grant applications to apply for upgrades / updates of existing equipment as well as some novel technology. The highest demand is currently for a new super-resolution microscope, which is luckily already funded by BBSRC, we are now in the process of testing the equipment to be purchased. Other demands stretched across a wide range of technologies and unfortunately also locations across the college, the committee tried to strike the best balance between all needs and decided to apply for the following package: * _New technology_: o an *automated high-throughput **m**icroscopy* system (e.g. Operetta or similar) o the high-throughput capacity, in combination with existing image processing / analysis capacity (e.g. Definiens) will satisfy the needs for both the high-content screening and to a large degree ImageStream needs * _Upgrade_: o *upgrade of the existing intravital microscope (FILM-CF3)* with options including high-sensitivity hybrid detectors, 405 laser, a cabinet for mouse handling, laser dispersion correction (detailed options to be checked with manufacturers) * _Support_: o *one full-time FILM staff post for Hammersmith* for the duration of the grant * _Replacement_: o *a high-sensitivity new-generation confocal* (similar to the Zeiss LSM-780 in Hammersmith), to be located in SAFB / South Kensington * _Possible options for small, complementary equipment add-ons_: o FleXcell Tensions System o ONIX microfluidic platform (if not already funded by other sources through other sources) o a high-precision multi-channel peristaltic pump system Obviously, we can't apply for everything on the list at the same time, some things will have to wait for the next equipment grant call. We now need to finalise the application - and for that *we need your support*: Those of you willing to support the application with your scientific interest and track record, please do get back to us soon - the deadline for the preliminary application is 2nd of December. And although the major bits of equipment to go on the application have been decided, if there are smaller add-ons missing on the list that would help with your microscopy in FILM, please let us know. Good imaging, Martin _*Information: *_ * http://www.wellcome.ac.uk/Funding/Biomedical-science/Funding-schemes/Strate… _*Summary of **m**icroscopy needs in Imperial College - FILM, feedback 2013*:_

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[FILM-Users 00489] Young Researchers in Life Sciences conference, May 26 to 28 in Institut Pasteur, Paris
by Alexandre Dufour 27 Mar '14

27 Mar '14

Hello everyone, My name is Alexandre and I’ve recently arrived in Jake Baum’s lab as a Visiting Scientist from Institut Pasteur in Paris. I’d like to let you know about the upcoming Young Researchers in Life Science (YRLS) conference end of may in Paris (flyer attached). It is organised by a federation of associations of young researchers (Msc/PhD/PostDocs) from all major life science institutes of Paris, but is open to anyone to attend. It welcomes roughly 200+ people every year, covering basically all areas in Life Sciences (it also includes special sessions and workshops, one of them on imaging this year) I happened to have co-founded and co-organised that congress for 3 years, and I can vouch that this conference is a great place to talk about your work (everyone gets to present a poster, talk if selected) and interact with other young researchers. The atmosphere is quite relaxed but very interdisciplinary, plus the science level is really high (best presentations get awarded), and each year at least 2 top-notch keynote speakers are invited. Since the idea is it to be open to be greatest number, it's very affordable (~30￡ including lunch and cocktail for 3-days), part of the budget is reserved for a few travel grants, and a couch-surfing system is available specifically between the conference participants. Deadline for short abstract submission is March 28 (tomorrow!), otherwise you may still register as “attendance only” until end of April. Don’t hesitate to transfer this mai;/flyer around in your respective circles/labs, every year more students come from abroad, and I hope the momentum continues. The website is www.yrls.fr, but feel free to let me know if you need more info. Alexandre — Alexandre Dufour, Ph.D. Visiting Researcher @ Jake Baum lab (www.baumlab.com) Department of Life Sciences, South Kensington campus Imperial College, London (UK) Permanent Researcher @ Biological Image Analysis group (www.bioimageanalysis.org) Department of Cell Biology & Infection Institut Pasteur, Paris (France) Begin forwarded message: > From: YRLS organizing team <contact(a)yrls.fr> > Subject: Registration closing soon: Young Researchers in Life Sciences Conference: 26-28th May > Date: 1 Mar 2014 14:37:34 GMT > To: undisclosed-recipients:; > > ***PLEASE FORWARD THIS EMAIL TO ALL THE PhDs AND POST-DOCS*** > > > > YOUNG RESEARCHERS IN LIFE SCIENCES CONFERENCE > > > The next edition of the YRLS meeting will take place at the world known Institut Pasteur, Paris, from May 26th to 28th. > > This conference is a venue for young scientists (PhDs and Post-Docs) from various fields in Life Sciences, to present their work, exchange ideas, learn from experts and form new collaborations. > > > > Early registration, with abstract submission: March 28th (LAST MONTH TO REGISTER!!!!!) > > Late registration (attendance only): APRIL 30th > > > > NOTE that if you are part of one of the organizing institute/association, the registration price is reduced. Don’t hesitate to contact your local representative, or us at participate.yrls(a)gmail.com > > Prizes will be awarded to the best presentations and the best posters. > > We are pleased to announce this year’s keynote speakers, Professor Karlheinz Meier and Benjamin Prud’homme, PhD. Prof. Meier is co-director of the EU Human Brain Project and Chair of the Department of Experimental Physics at the University of Heidelberg, Germany. Dr. Benjamin Prud’homme, a group leader at the Institut de Biologie du Développement de Marseille Luminy, is interested in understanding the genetic and developmental bases of phenotypic novelty. > > > Please visit our website for more information : http://yrls.fr/

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[FILM-Users 00488] Young Researchers in Life Sciences conference, May 26 to 28 in Institut Pasteur, Paris
by Alexandre Dufour 27 Mar '14

27 Mar '14

Hello everyone, My name is Alexandre and I’ve recently arrived in Jake Baum’s lab as a Visiting Scientist from Institut Pasteur in Paris. I’d like to let you know about the upcoming Young Researchers in Life Science (YRLS) conference end of may in Paris (flyer attached). It is organised by a federation of associations of young researchers (Msc/PhD/PostDocs) from all major life science institutes of Paris, but is open to anyone to attend. It welcomes roughly 200+ people every year, covering basically all areas in Life Sciences (it also includes special sessions and workshops, one of them on imaging this year) I happened to have co-founded and co-organised that congress for 3 years, and I can vouch that this conference is a great place to talk about your work (everyone gets to present a poster, talk if selected) and interact with other young researchers. The atmosphere is quite relaxed but very interdisciplinary, plus the science level is really high (best presentations get awarded), and each year at least 2 top-notch keynote speakers are invited. Since the idea is it to be open to be greatest number, it's very affordable (~30￡ including lunch and cocktail for 3-days), part of the budget is reserved for a few travel grants, and a couch-surfing system is available specifically between the conference participants. Deadline for short abstract submission is March 28 (tomorrow!), otherwise you may still register as “attendance only” until end of April. Don’t hesitate to transfer this mai;/flyer around in your respective circles/labs, every year more students come from abroad, and I hope the momentum continues. Please feel free to let me know if you need more info. Alexandre — Alexandre Dufour, Ph.D. Visiting Researcher @ Jake Baum lab (www.baumlab.com) Department of Life Sciences, South Kensington campus Imperial College, London (UK) Permanent Researcher @ Biological Image Analysis group (www.bioimageanalysis.org) Department of Cell Biology & Infection Institut Pasteur, Paris (France) Begin forwarded message: > From: YRLS organizing team <contact(a)yrls.fr> > Subject: Registration closing soon: Young Researchers in Life Sciences Conference: 26-28th May > Date: 1 Mar 2014 14:37:34 GMT > To: undisclosed-recipients:; > > ***PLEASE FORWARD THIS EMAIL TO ALL THE PhDs AND POST-DOCS*** > > > > > > YOUNG RESEARCHERS IN LIFE SCIENCES CONFERENCE > > > The next edition of the YRLS meeting will take place at the world known Institut Pasteur, Paris, from May 26th to 28th. > > This conference is a venue for young scientists (PhDs and Post-Docs) from various fields in Life Sciences, to present their work, exchange ideas, learn from experts and form new collaborations. > > > > Early registration, with abstract submission: March 28th (LAST MONTH TO REGISTER!!!!!) > > Late registration (attendance only): APRIL 30th > > > > NOTE that if you are part of one of the organizing institute/association, the registration price is reduced. Don’t hesitate to contact your local representative, or us at participate.yrls(a)gmail.com > > Prizes will be awarded to the best presentations and the best posters. > > We are pleased to announce this year’s keynote speakers, Professor Karlheinz Meier and Benjamin Prud’homme, PhD. Prof. Meier is co-director of the EU Human Brain Project and Chair of the Department of Experimental Physics at the University of Heidelberg, Germany. Dr. Benjamin Prud’homme, a group leader at the Institut de Biologie du Développement de Marseille Luminy, is interested in understanding the genetic and developmental bases of phenotypic novelty. > > > Please visit our website for more information : http://yrls.fr/ > > Hope to see you there > > Regards > > Cyril PICARD > > > > > On behalf of the YRLS 2014 Team > May 26-28, 2014 , Institut Pasteur > contact(a)yrls.fr > www.yrls.fr > > > >

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[FILM-Users 00487] cancelled FILM Club
by Martin Spitaler 26 Mar '14

26 Mar '14

Dear microscopists, unfortunately this month's FILM Club (due today) had to be cancelled, because the speaker pulled out short-notice and we didn't find a replacement - sorry. The next FILM Club will be on Wednesday 30 April (SAFB-122), Amanda Wilson (Engineering) will talk about "The Histocutter: A revolution in 3D imaging". For more details see FILM website / NEWS / FILM CLUB <http://www3.imperial.ac.uk/imagingfacility/news#filmclub>. Good imaging, Martin >> http://www3.imperial.ac.uk/imagingfacility/news#filmclub -- ------------------------------------------------------------------------ *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 00486] Fwd: Release of OME Consortium Projects
by Martin Spitaler 14 Mar '14

14 Mar '14

...forwarded for your information; some interesting new tools are are in there, e.g. FLIMfit for improved fluorescence lifetime analysis or content-based image searching, Martin *Subject:* Release of OME Consortium Projects *From:* Jason Swedlow <jrswedlow(a)GMAIL.COM> *Reply-To:* Confocal Microscopy List <CONFOCALMICROSCOPY(a)LISTS.UMN.EDU> *Date:* Thu, 13 Mar 2014 15:27:58 +0000 *Content-Type:* text/plain ***** To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ***** Dear All, Today we are releasing several "Projects" from the OME Consortium which add extra functionality and are fully compatible with the newly released OMERO and Bio-Formats 5.0.0. The Projects included in this release are: *FLIMfit 4.6.4* Mac-only, Windows version to follow FLIMfit is now compatible with OMERO 5.0.0 and features support for LaVision Imspector .msr files via Bio-Formats 5.0.0; Support for Becker& Hickl SPCImage .sdt files has been extended to include measurement mode 13; Download fromhttp://downloads.openmicroscopy.org/flimfit/4.6.4/ *u-track 2.1.1* u-track now supports OMERO 5.0.0 and is bundled with Bio-Formats 5.0.0; Improvements include new graphical interfaces to login and browse data onto an OMERO server; Download fromhttp://downloads.openmicroscopy.org/u-track/2.1.1/ *OMERO.webtagging 1.0.0* First full release of this application. OMERO.webtagging provides a semi-automatic process for creating and applying tags based on the filename, path and extension of the original data. Improvements over the beta version include support for displaying all existing tags, tighter webclient integration and some performance enhancements. Download fromhttp://downloads.openmicroscopy.org/webtagging/1.0.0/ *OMERO.figure 1.0.0-beta1* OMERO.figure is a new web app for creating figures from images in OMERO. It has tools for quickly aligning panels, adjusting rendering settings, scrolling Z and T, adding labels and displaying scalebars. Images can be exported as PDF or saved and shared via the web. Seehttp://will-moore.github.io/figure/ for more information. This is a beta release; feedback and comments welcome! Download fromhttp://downloads.openmicroscopy.org/figure/1.0.0-beta1/ *OMERO.mtools 1.0.0* OMERO.mtools is a suite of MATLAB-based tools for carrying out common image analysis tasks on images stored in an OMERO.server; it has its own GUI and only requires an installation of MATLAB Compiler Runtime to run. OMERO.mtools has been used to analyse data for several papers published by groups in Dundee; comments and feedback welcome! Download fromhttp://downloads.openmicroscopy.org/mtools/1.0.0/ *OMERO.searcher 0.1.0* OMERO.searcher provides the ability to search for images in OMERO by their content (e.g., subcellular patterns) rather than just by their annotations. This is an early preview release, not intended for production use. Comments and feedback welcome! Download fromhttp://downloads.openmicroscopy.org/searcher/0.1.0/ *OMERO.csvtools 0.2.2* OMERO.csvtools is a script-based tool for mass tagging operations; Tag definitions are supplied in a simple, conventional CSV structure, and may be provided through a local file on disk or fetched remotely from an OMERO.server file store. This is a preview release, comments and feedback welcome! Download fromhttps://bintray.com/imagopole/omero/omero-csv-tools/ These projects are available to download at: http://downloads.openmicroscopy.org/ Further information for each project is available at: http://www.openmicroscopy.org/site/products/partner The OME Consortium will keep on maintaining and developing these applications. Any problems or comments, please use the OME Forums or mailing lists: http://www.openmicroscopy.org/site/community Regards, The OME Team -- ************************** Centre for Gene Regulation& Expression College of Life Sciences MSI/WTB/JBC Complex University of Dundee Dow Street Dundee DD1 5EH United Kingdom phone (01382) 385819 Intl phone: 44 1382 385819 FAX (01382) 388072 email: jrswedlow(a)dundee.ac.uk Lab Page:http://www.lifesci.dundee.ac.uk/gre/staff/jason-swedlow Open Microscopy Environment:http://openmicroscopy.org

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[FILM-Users 00485] Fwd: FW: [sbcf] 3D Electron Microscopy meeting Announcement
by Martin Spitaler 13 Mar '14

13 Mar '14

...forwarded for your information, Martin -------- Original Message -------- Subject: FW: [sbcf] 3D Electron Microscopy meeting Announcement Date: Tue, 11 Mar 2014 10:23:11 +0000 From: Braga, Vania M M <v.braga(a)imperial.ac.uk> To: Spitaler, Martin <m.spitaler(a)imperial.ac.uk> Hi Martin This may be of interest to FILM users Best Vania Vania Braga, PhD Campus Director, South Kensington, Faculty of Medicine Reader in Cell-cell Adhesion Signaling Molecular Medicine National Heart and Lung Institute Faculty of Medicine Imperial College London Sir Alexander Fleming Building SW7 2AZ  +44 20 7594-3233 (office) +44 20 7594-3109 (lab)  +44 20 7594-3100  v.braga(a)imperial.ac.uk -----Original Message----- From: sbcf-request(a)listes.univ-rennes1.fr [mailto:sbcf-request@listes.univ-rennes1.fr] On Behalf Of Michaël Trichet Sent: 10 March 2014 17:26 To: sbcf(a)listes.univ-rennes1.fr; gregoire.michaux(a)univ-rennes1.fr Subject: [sbcf] 3D Electron Microscopy meeting Announcement Dear all, It is a pleasure to announce the 1st International Meeting entitled "3D Electron Microscopy: From Molecule to Organism", organized by the Cellular Imaging Network of Université Pierre et Marie Curie. It will take place on May, 22nd and 23rd in Paris at the Institut du Cerveau et de la Moelle épinière (CHU Pitié-Salpétrière). For registration and abstract submission, please, follow this link: http://www.imageriecellulaire.upmc.fr This Meeting will present state-of-the-art 3-dimensional techniques in electron microscopy, treating a combination of leading approaches with various model organisms. In this Meeting, we will particularly focus on techniques covering molecular and macromolecular components, cells, complex tissues and organisms: - electron tomography - serial imaging (FIB/SEM, Serial Block Face) - cryo-EM - Scanning Electron Microscopy - single-particle analysis - image processing The program includes selected flash presentations, posters sessions and booth organization by leading companies in the field. Regards The scientific committee: Claude-Marie Bachelet (ICM) Anne Baron-Van Evercooren (ICM) Alain Trembleau (IBPS) Michaël Trichet (IBPS) Catherine Vénien-Bryan (IMPMC) Chers collègues, J'ai le plaisir de vous annoncer que le réseau d’Imagerie Cellulaire de l’Université Pierre et Marie Curie organise son 1er Colloque International intitulé « 3D Electron Microscopy: From Molecule to Organism ». Il aura lieu les 22 et 23 Mai 2014 à Paris à l’Institut du Cerveau et de la Moelle épinière (CHU Pitié-Salpétrière). Les inscriptions et la soumission des résumés sont accessibles sur le site du Réseau : http://www.imageriecellulaire.upmc.fr Le colloque présentera à la communauté des biologistes les techniques les plus récentes pour l’imagerie en trois dimensions en microscopie électronique. Sa force est d'associer des techniques de pointe à la diversité des systèmes étudiés en biologie. Nous nous sommes focalisés sur les techniques étudiant le vivant selon tous ses niveaux d’organisation, des molécules et complexes multimoléculaires aux tissus et organismes : - tomographie électronique - serial imaging (FIB/SEM, Serial Block Face) - cryo-EM - Microscopie Electronique à Balayage - Particules isolées - reconstruction d’images Le programme prévoit des présentations courtes sélectionnées, des sessions de posters et des stands dédiés aux constructeurs et fournisseurs partenaires. Bien cordialement Le Comité d'Organisation : Claude-Marie Bachelet (ICM) Anne Baron-Van Evercooren (ICM) Alain Trembleau (IBPS) Michaël Trichet (IBPS) Catherine Vénien-Bryan (IMPMC) -- Michaël Trichet Service de Microscopie Electronique IBPS / Institut de Biologie Paris-Seine Université P. et M. Curie Bâtiment B, 7ème étage, case courrier 25 7-9, quai St Bernard 75252 PARIS cedex 05 Tel. : + 33 (0) 1 44 27 25 53 Fax. : + 33 (0) 1 44 27 22 91 http://www.ifr83.upmc.fr/

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[FILM-Users 00484] Fwd: [lsr-group] kcl - smlms2014
by Martin Spitaler 13 Mar '14

13 Mar '14

...forwarded for your information, an interesting meeting being organised by the super-res people in Kings College, Martin -------- Original Message -------- Subject: [lsr-group] kcl - smlms2014 Date: Thu, 13 Mar 2014 06:46:21 +0000 From: Owen, Dylan <dylan.owen(a)kcl.ac.uk> To: 'lsr-group(a)imperial.ac.uk' <lsr-group(a)imperial.ac.uk> Dear colleague, the abstract submission site for the Single Molecule Localisation Microscopy Symposium 2014 is now open! Please find it on the SMLMS2014 website: http://www.kcl.ac.uk/biohealth/newsevents/eventrecords/2014/aug/smlms-2014.… As the participant number is limited to 80, so please sign up soon! A number of short talks will be selected from the submitted abstracts. The preliminary program is now available on the website. Registration cost are £200 for students and £350 for academics. Accommodation, lunch and dinner are included in this amount. We are looking forward to an exciting meeting and hope to see you there. Please inform colleagues that may be interested in this meeting as well. With best regards, The organizers ------------------------------- SMLMS 2014 4th Single Molecule Localization Microscopy Symposium August 27th to 29th 2014 King's College London Organizing committee: Helge Ewers -<mailto:helge.ewers at kcl.ac.uk <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group>> helge.ewers at kcl.ac.uk <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group><mailto:hewers at ethz.ch <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group>> Aleksandra Radenovic -aleksandra.radenovic at epfl.ch <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group><mailto:aleksandra.radenovic at epfl.ch <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group>> Mike Heilemann -Heilemann at chemie.uni-frankfurt.de <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group><mailto:Heilemann at chemie.uni-frankfurt.de <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group>> smlms2014 at kcl.ac.uk <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group><mailto:smlms2014 at kcl.ac.uk <https://mailman.ic.ac.uk/mailman/listinfo/lsr-group>> http://www.kcl.ac.uk/biohealth/newsevents/eventrecords/2014/aug/smlms-2014.… **

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[FILM-Users 00483] Fwd: Upgrade to OMERO 5?
by Martin Spitaler 03 Mar '14

03 Mar '14

Dear microscopists, tomorrow we are planning an upgrade of OMERO to version 5 (Mark Woodbridge's email from BSS). If anyone is planning to use OMERO tomorrow morning, please let Mark know. The background of this: OMERO 5 has completed changed the way it's handling image data: Rather than importing (and duplicating) the original pixel data, it now _*MOVES*_ the _*ORIGINAL FILES*_//(in whatever format they are in, Leica LIF, Zeiss CZI, ....) _*to the backed-up storage space*_, it just reads the metadata (microscope type, lasers, lenses, filters, dimensions etc.) and writes them into the OMERO database. Advantages: * _*no data *__*duplication anymore*_, only _one_ version is saved (not original file format + OMERO format) = saving space and money * it should be much _*faster*_ (we still need to test how much faster) for large data files, because data are only read and written once * the original files will be on the server, so there is _*no risk of losing information*_ (as before, if the original files were not uploaded to save space) * the original files will also be available directly to any other software - this will be useful straight away for FIJI scripts, Definiens analysis and very soon Zeiss ZEN (for which we will get a server licence as part of the super-resolution data setup) Of course, this is how OMERO should have worked from the beginning (it's been a long and painful discussion to get such a profound change for an established system), but we now have high hopes that this will massively help with our data. Because now, if you follow our recommendation to delegate storage and backup to the Bioinformatics Support Service, there is really no excuse left for leaving them on quickly ageing DVDs, harddrives, ... If you use OMERO, it will probably help you finding your data later, but even if not, this is still by far the best way to keep your data safe, and well worth 1-2% of your grant money. Good imaging, Martin -------- Original Message -------- Subject: Re: Status of upgrade to OMERO 5? Date: Mon, 3 Mar 2014 11:06:35 +0000 From: Mark Woodbridge <m.woodbridge(a)imperial.ac.uk> To: French, Paul (PHOT) M W (Photonics) <paul.french(a)imperial.ac.uk>, Munro, Ian <i.munro(a)imperial.ac.uk> CC: Butcher, Sarah A <s.butcher(a)imperial.ac.uk>, Dunsby, Christopher W <christopher.dunsby(a)imperial.ac.uk>, Alexandrov, Yuriy <y.alexandrov(a)imperial.ac.uk>, Martin Spitaler <m.spitaler(a)imperial.ac.uk> Hi all, I am planning to attempt the OMERO 5 upgrade tomorrow morning (the 4th) from 9am, meaning that the system may be unavailable until lunchtime. Please let me know today if this will cause any problems. Thanks, Mark.

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