May 2011 - FILM-Users - imperial.ac.uk

[FILM-Users 00076] TODAY: FILM Club
by Martin Spitaler 27 May '11

27 May '11

...just a reminder about the FILM-Club TODAY, Martin > > > Dear microscopists, > > sorry for the late notice, there were some problems with the > organisation, but this Friday it's time for the FILM Club again: > > FILM Club May 2011: > Amir Horowitz: Live cell imaging of particle capturing during apoptosis > > Friday 27 May 2011, SAFB-121 > > Amir Horowitz is presenting his project which is based on a combination > of confocal imaging, 3D image analysis and mathematical modelling to > understand biological and physical mechanisms behind the process of > phagocytosis. > > This is going to be an interesting talk for many of us, either working > on phagocytosis, or generally interested in the combination of tools to > understand biology. > > > 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 > Website: http://imperial.ac.uk/imagingfacility > > > _______________________________________________ > FILM-Users mailing list > FILM-Users(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/film-users

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[FILM-Users 00075] Fwd: Dyes
by Martin Spitaler 26 May '11

26 May '11

...can anyone help Florencia? If so, please contact her directly, Martin -------- Original Message -------- Subject: Dyes Date: Tue, 24 May 2011 12:09:07 +0100 From: Minuzzi, Florencia <florencia.minuzzi05(a)imperial.ac.uk> To: Spitaler, Martin <m.spitaler(a)imperial.ac.uk> Dear Martin, I’m trying to look at the ER in my cells, and I think DiOC6 is probably the best dye to use in yeast. Do you have any that I could borrow to try before I buy it? The catalogue number is D-273. Thanks, Florencia

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[FILM-Users 00074] Fwd: FILM Club this Friday
by Martin Spitaler 24 May '11

24 May '11

Sorry, I forgot the time: As usual, it's 1PM, this Friday SAFB-121, Martin -------- Original Message -------- Subject: FILM Club this Friday Date: Tue, 24 May 2011 17:47:55 +0100 From: Martin Spitaler <m.spitaler(a)imperial.ac.uk> To: film-users <film-users(a)imperial.ac.uk> Dear microscopists, sorry for the late notice, there were some problems with the organisation, but this Friday it's time for the FILM Club again: FILM Club May 2011: Amir Horowitz: Live cell imaging of particle capturing during apoptosis Friday 27 May 2011, SAFB-121 Amir Horowitz is presenting his project which is based on a combination of confocal imaging, 3D image analysis and mathematical modelling to understand biological and physical mechanisms behind the process of phagocytosis. This is going to be an interesting talk for many of us, either working on phagocytosis, or generally interested in the combination of tools to understand biology. 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 Website: http://imperial.ac.uk/imagingfacility

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[FILM-Users 00073] FILM Club this Friday
by Martin Spitaler 24 May '11

24 May '11

Dear microscopists, sorry for the late notice, there were some problems with the organisation, but this Friday it's time for the FILM Club again: FILM Club May 2011: Amir Horowitz: Live cell imaging of particle capturing during apoptosis Friday 27 May 2011, SAFB-121 Amir Horowitz is presenting his project which is based on a combination of confocal imaging, 3D image analysis and mathematical modelling to understand biological and physical mechanisms behind the process of phagocytosis. This is going to be an interesting talk for many of us, either working on phagocytosis, or generally interested in the combination of tools to understand biology. 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 Website: http://imperial.ac.uk/imagingfacility

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[FILM-Users 00072] Definiens training course
by Martin Spitaler 20 May '11

20 May '11

Dear microscopists, I'm planning to organise another training course for the Definiens advanced image analysis software this summer. If you are interested in such a course, please let me know, content and dates of the course are flexible and depend on the requirements of participants. If there is enough interest, I hope of organising a basic course for beginners and an advanced version for more experience users. The costs for the course should be ~£400 per participant. The Definiens software gives biologists relatively easy access to very complex image analysis tools. Since we installed it about a year ago, we have very successfully used it for a large range of microscopy images in the facility (the largest analysis was on a dataset of 30,000 images). Unlike Volocity, the software doesn't provide quick drag&drop solutions for simple tasks, but for anything more demanding it provides a huge set of tools to identify objects in crowded and noisy microscopy images, taking into account biological information, and extract a large range of features about intensity, shape, position, orientation, density, boundaries, .... of objects. If you are interested, please get in contact with me. If you want more information, have a look at the links on the FILM website / Equipment / Definiens (http://www3.imperial.ac.uk/portal/page/portallive/imagingfacility/equipment…) or on the Definiens Community website (http://community.definiens.com/home.html) 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 Website: http://imperial.ac.uk/imagingfacility

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[FILM-Users 00071] Fwd: ibidi Online LIVE Webinar - 18th May...
by Martin Spitaler 17 May '11

17 May '11

...for your information, Martin -------- Original Message -------- Subject: ibidi Online LIVE Webinar - 18th May... Date: Mon, 16 May 2011 16:13:18 +0100 From: James Smith <James(a)thistlescientific.co.uk> Reply-To: James(a)thistlescientific.co.uk <James(a)thistlescientific.co.uk> To: Spitaler, Martin <m.spitaler(a)imperial.ac.uk> To view as a webpage, click here <http://www.thistlescientific.co.uk/e-news/ibidi-may/ibidi-may.html> Visit our website <http://www.thistlescientific.co.uk> Contact us <http://www.thistlescientific.co.uk/acatalog/contact_us.html> *Immunofluorescence <http://www.ibidi.de/products/disposables/S_8060X_SlideVI.html>Angiogenesis <http://www.ibidi.de/products/disposables/S_8015X_Slide_Angio.html>Flow assays <http://www.ibidi.de/products/instruments/I_109XX_ibidi_pump.html>Life Cell Imaging <http://www.ibidi.de/products/disposables/D_811XX_Dish35mm_high.html>* */Chemotaxis <http://www.ibidi.de/products/disposables/S_8030X_Slide_Chemo.html>Wound Healing <http://www.ibidi.com/products/disposables/E_802XX_CI_family.html>Gene Transfection <http://www.ibidi.de/products/reagents/R_606XX_TransfKitVI.html>/* /Live Webinar:/ /Principles and Basics of Light Microscopy for Cell-Based Assays/ /During the last decade, the imaging of cultured, or primary, cells has played a major role in helping to understand biological processes. Cell-based assays use light microscopy as one of the most dominant parameters in the visualization of multi-parameter data sets./ /In this webinar we will present the basics of microscopy starting with the inner workings of modern microscopes. We will also discuss the optical properties of glassware and Petri dishes, including the underlying physics. Finally, you will learn about the principles of fluorescence microscopy techniques and modern live cell imaging, using specially designed ibidi -Slides and -Dishes. / /**Register now for your preferred date*:*/ * // /*>> May 18, 2011, 8 am BST (3 pm Taiwan | 4 pm Tokyo | 5 pm Sydney) <http://www.ibidi.de/db_webinars/webinar_mb_20110518_8amCET.php>* / * /*>> May 18, 2011, 1 pm BST <http://www.ibidi.de/db_webinars/webinar_mb_20110518_2pmCET.php>* / * /*>> May 18, 2011, 4 pm BST (11 am EDT | 10 am CDT | 8 am PDT) <http://www.ibidi.de/db_webinars/webinar_mb_20110518_5pmCET.php>* / /*This webinar will focus on the following topics:* / * // /Basics of light microscopy (e.g. optical properties and cover slips) / * /Practical aspects and applications (e.g. Khler illumination and contrast techniques) / * /Fluorescence microscopy / * /Live cell imaging applications / /* */ /Principles and Basics of Light Microscopy for Cell-Based Assays/ /*Elias Horn, ibidi GmbH*/ /Elias Horn studied biotechnology at the University of Applied Science, Mittweida. Since 2004, he has been working on the development of customer-specific slides, for /in vivo/ cell culture experiments, in the Research and Development department at ibidi. His main focus is the design and implementation of migration and chemotaxis assays./ // /For further information on any of our products, contact 01698 338844, or to browse our catalogue visit www.thistlescientific.co.uk <http://www.thistlescientific.co.uk>./ /Thistle Scientific - DFDS House - Goldie Road - Uddingston- GLASGOW - G71 6NZ/ /TEL: 01698 338844 - FAX: 01698 338880 - MAIL: info(a)thistlescientific.co.uk <mailto:info@thistlescientific.co.uk>/ /*********************************************************************************************************************************************************** To unsubscibe click here <http://www.thistlescientific.co.uk/acatalog/newsletter-feedback.html> / /***********************************************************************************************************************************************************/ //

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[FILM-Users 00070] MICROSCOPY DAY 2011
by Martin Spitaler 17 May '11

17 May '11

Dear microscopists, this year we are are having a microscopy day again, a whole day of lectures, presentations and demonstrations about microscopy: MICROSCOPY DAY, MONDAY 20 JUNE 2011, 9.45-17.00, SAFB-G34 Following up and expending on the successful event two years ago, we are offering information from the very basics to the highly sophisticated, from fluorophores to image analysis. The details are still being finalised, if you are interested in a particular topic please let me know. PRELIMINARY PROGRAMME: 9.45- 9.50 Introduction 9.50-10.30 Basics of microscopy: properties of light, diffraction limit, resolution, contrast methods, epifluorescence, confocal, ... 10.30-11.15 Principles of fluorescence: fluorophores, photo-bleaching, photo-switching, phototoxicity, ... 11.15-11.30 coffee 11.30-12.15 Special techniques I: two photon microscopy, second harmonic generation, in vivo imaging, Flim, Fret, ... 12.15-13.00 Special techniques II: high-resolution microscopy (TIRF, PALM, STORM), ... 13.00-14.30 lunch break and demonstrations: - TIRF, PALM, STORM - 2P, SHG, in vivo, Flim - tour of EM facility - OMERO image database, XperimentR - image analysis tools 14.30-15.15 Transmission electron microscopy 15.15-16.00 Understanding and handling images: data formats, pixel and metadata, visualisation, OMERO database, analysis workflow, ... 16.00-16.15 coffee 16.15-17.00 Tools for image analysis: filtering, edge detection, segmentation, feature extraction, morphoplogy, ... For more details and updates, see FILM website / NEWS (http://www3.imperial.ac.uk/portal/page/portallive/imagingfacility/news) Everybody is welcome. see you there, and 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 Website: http://imperial.ac.uk/imagingfacility

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[FILM-Users 00069] Fwd: stains
by Martin Spitaler 16 May '11

16 May '11

...can anyone help Gerard? Martin -------- Original Message -------- Subject: stains Date: Mon, 16 May 2011 11:24:37 +0100 From: Bishop, Gerard J <g.bishop(a)imperial.ac.uk> Dear Martin/Ian (Fiona) Are you aware of anyone having these stains? We want to try them for looking at trichomes Safranin O Sudan Red B Sudan Black B Chlorozol Black E Periodic acid-schiff Ruthenium Red Osmium Tetroxide Cheers Gerard Gerard Bishop Division of Biology 509- SAF Building Imperial College London South Kensington Campus London SW7 2AZ UK http://www3.imperial.ac.uk/people/g.bishop ph. +44-20759-46482

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[FILM-Users 00068] Fwd: [neuroscience-technology-network] ISN Talk: John Tsotsos on Active Visual search, EEE-611, 23 May, at 14:00
by Martin Spitaler 13 May '11

13 May '11

...for your information, a talk related to the wider area of image analysis, Martin -------- Original Message -------- Subject: [neuroscience-technology-network] ISN Talk: John Tsotsos on Active Visual search, EEE-611, 23 May, at 14:00 Date: Thu, 12 May 2011 13:45:25 +0100 From: Demiris, Yiannis <y.demiris(a)imperial.ac.uk> Dear colleagues, Professor John Tsotsos, York University in Toronto, Canada, will be visiting Imperial on the afternoon of the 23rd of May. He will be giving a talk on "Active Visual Search" at the Gabor Seminar room (EEE-611), Department of Electrical and Electronic Engineering. Professor Tsotsos holds the Canada Research Chair in Computational Vision at York University, and is a Fellow of the Royal Society of Canada. Abstract and speaker bio below. All welcome! With best wishes, Yiannis ------------- Active Visual Search Professor John K. Tsotsos Department of Computer Science and Engineering Centre for Vision Research York University, Toronto, Canada Monday 23 May 2011, 1400-1500 Denis Gabor Seminar Room (611), EEE Department Abstract: Active perception uses intelligent control strategies applied to the data acquisition process that depend on the current state of data interpretation and has a history that pre-dates computer vision. I will very briefly lay out this history and detail theoretical arguments on the computational nature of the general problem. The theory informs us that optimal solutions are not likely to exist. In this context, I consider the problem of visually finding an object in a mostly unknown space with a mobile robot. It is clear that all possible views and images cannot be examined in a practical system and as a result, this is cast as an optimization problem. The goal is to optimize the probability of finding the target given a fixed cost limit in terms of total number of robotic actions required to find the visual target. Due to the inherent intractability of this problem, we present an approximate solution and investigate its performance and properties. This has been successfully implemented on three different robots, the most recent being Hondas ASIMO and examples of its performance will be shown. If anyone wishes to see background papers for this, they can look at: Andreopoulos, A., Wersing, H., Janssen, H., Hasler, S., Tsotsos, J.K., Körner, E., Active 3D Object Localization using a Humanoid Robot, IEEE Transactions on Robotics, 27(1), p47-64, 2011. Shubina, K., Tsotsos, J.K. Visual Search for an Object in a 3D Environment using a Mobile Robot, Computer Vision and Image Understanding, 114, p535-547, 2010. Ye, Y., Tsotsos, J.K., A Complexity Level Analysis of the Sensor Planning Task for Object Search, Computational Intelligence, 17(4), p605-620, Nov. 2001. Ye, Y., Tsotsos, J.K., Sensor Planning for Object Search, Computer Vision and Image Understanding 73(2), p145-168, 1999. About the speaker: Professor John K. Tsotsos, Fellow of the Royal Society of Canada and Distinguished Research Professor of Vision Science, holds the Canada Research Chair in Computational Vision at York University, as well as Adjust professorships at the Department of Ophthalmology and Visions Sciences at the University of Toronto. His research focuses on three main themes: visual attention in humans and computer systems, visually guided mobile robotics and computer vision. He has published numerous papers in multiple disciplines including computer science, attention, computational neuroscience, computer vision and robotics, and he is the author of an upcoming MIT press book A Computational Perspective on Visual Attention. --- Dr Yiannis Demiris, Senior Lecturer, Intelligent Systems and Networks Group, Department of Electrical and Electronic Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2BT, London, UK Tel: +44(0)2075946300, Fax: +44(0)2075946274 http://www.iis.ee.imperial.ac.uk/yiannis

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[FILM-Users 00067] Fwd: Jaroslav Stark Memorial Meeting July 13th 2011 - Systems Biology & Bioinformatics
by Martin Spitaler 11 May '11

11 May '11

...for your information -------- Original Message -------- Subject: Jaroslav Stark Memorial Meeting July 13th 2011 - Systems Biology & Bioinformatics Date: Wed, 11 May 2011 10:25:01 +0100 From: Bioinformatics <bioinformatics(a)imperial.ac.uk> Please circulateas appropriate within your Departments. */Imperial College London /* *//* */Centre for Integrative Systems Biology & Bioinformatics (CISBB) Open Day/* */with/* */Jaroslav Stark Memorial Session/* // /10:00 – 18:00 Wednesday July 13^th 2011 / /Skempton Lecture Theatre, Skempton Building, / /South Kensington campus/ /London SW7 2AZ/ // // /This meetings marks the opening of CISBB – the merger of the Centre for Integrative Systems Biology (CISBIC) and The Centre for Bioinformatics / // /Opening: / Sir Keith O’Nions, Rector // Prof Michael Sternberg (Centre Director) /Session 1: Bioinformatics & Systems Biology/ Dr Ewan Birney (EBI) Dr John Pinney (Imperial) Prof Nir Friedman (Weizmann) Prof Cardelli (Microsoft, Cambridge) Dr Robert Endres (Imperial) Prof Frank Jülicher (MPI Dresden) // /Session 2: Jaroslav Stark Memorial Session / Opened by Prof Maggie Dallman (Imperial): Prof Tom Kirkwood (Newcastle) Prof Robin Callard (UCL) // ** *To attend please register at **http://www.bioinformatics.ic.ac.uk/cisbb/**- **registration**is free **and all are welcome.* ** ** *For further information, please contact **bioinformatics(a)imperial.ac.uk* <mailto:bioinformatics@imperial.ac.uk>** ********************************************* Centre for Bioinformatics (Post to:- Biochemistry Building) Division of Molecular Biosciences Faculty of Natural Sciences Imperial College London SW7 2AZ,UK bioinformatics(a)imperial.ac.uk <mailto:bioinformatics@imperial.ac.uk> www.imperial.ac.uk/bioinformatics <http://www.imperial.ac.uk/bioinformatics> (Centre) _www3.imperial.ac.uk/cisbic_(CISBIC) Tel +44 (0)20 7594 5715; Fax +44 (0)20 7594 5789 ****************************************************************

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