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

[FILM-Users 00092] Definiens training dates
by Martin Spitaler 13 Sep '11

13 Sep '11

Dear microscopists, it's been tricky to find a common date between room and all people involved, and it's now later than originally planned, but now the Definiens Basic training is now fixed: Training course: Definiens Basic I Time & date: Tue 27 - Thu 29 September 2011, 10.00-17.00 Location: Computer Training Room in the Central Library, 2nd floor (South Kensington Campus) Trainer: Thomas Mrowiec, Definiens Available places is 6-10 Costs: max £500 (based on 6 participants, cheaper with more) Definiens Developer XD: We have had this software in the facility for just over a year now, and it's already proved its value for some very challenging image analysis projects which would have been impossible for us otherwise (the most demanding of them the fully automated quantification of immunological synapse formation in 30,000 time frames). The software offers easy access to a huge range of image analysis tools, and is specialised in analysing images on multiple scales, taking the biological context into account. I don't have any shares in the company, but it's just extremely useful, and with a good introduction - like this training course - pretty straightforward to use (recently a user with no experience in image analysis commented 'this is much easier than ImageJ'). I have also noticed that this training course is an excellent entry into the complex field of image analysis, whatever software tool you are using in the future. Trainer and training: Thomas Mrowiec comes from the Definiens Academy, specialising in customer training. The training comes with very detailed training material and sample datasets, and it doesn't require any previous experience. However, users are welcome to bring along their own sample images and get ideas how best to start with their analysis. Arranging the training on-site here we are able to keep the costs to a minimum (no travelling or accomomdation costs, larger number of participants). If you are interested, please book and confirm your place as soon as possible. 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 00091] Changes to booking for Additional Hardware Requests
by Rothery, Stephen M 29 Jul '11

29 Jul '11

Dear all Please note we have changed the way additional hardware is requested: https://workspace.imperial.ac.uk/imagingfacility/Public/additional%20hardwa… FILM - additional hardware request SharePoint booking page: https://sharepoint.ic.ac.uk/FoM/NHLI/Facilities/FILM/Lists/FILM%20Hardware%… Many thanks Steve ************************************************************** Steve Rothery Laboratory Manager Cardiovascular Sciences (Brompton Campus), National Heart & Lung Institute Imperial College London Guy Scadding Building Dovehouse Street London SW3 6LY Tel 020 7352 8121 ext 3317 And: FILM - Facility for Imaging by Light Microscopy FILM Technician Sir Alexander Fleming Building, desk 403 Imperial College London / South Kensington Exhibition Road London SW7 2AZ Tel. +44-(0)207 594 9793 E-mail s.rothery(a)imperial.ac.uk Website: http://imperial.ac.uk/imagingfacility **************************************************************

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[FILM-Users 00090] new FILM server
by Martin Spitaler 29 Jul '11

29 Jul '11

Dear microscopists, we have now purchased our own file server dedicated for FILM data, replacing the old '\\icfs19\imagingfacility' share (formerly mapped as 'drive X:'). This should be very fast and much larger, so hopefully for the time being it will solve data transfer problems. As before, this file server is to be used as scratch disk for file transfer only, NOT to store any data. We have more and more experiments producing up to a few hundred GB in one go, particularly in live imaging and PALM / STORM microscopy, so even the larger file server would fill up quickly. Unfortunately the 'total space' and 'free space' information is wrong, because this refers to the total server size, but much of it is used for FILM administration and backup (e.g. of microscope computer installations). For secure, long-term storage you are advised to use the dedicated OMERO image database (see FILM website / LINKS for details). Therefore, our data policy is still the same: # users are responsible for their own data # data on the FILM server can be deleted at any time without warning # data on microscope computers are regularly deleted after 3 months (but it has happened before that someone has mistakingly deleted data earlier) Recommended workflow for data storage: # after acquisition, copy them to the FILM server (or upload them directly to OMERO, if the data size is small) # from your own computer, upload them to OMERO (or copy them to your own safe storage space) # then delete them from the microscope computer and FILM server ACCESS TO THE NEW FILM SERVER (see also FILM website > Facility Guidelines > Data & Network > Access to the file server) # open MY COMPUTER # in the menu, select TOOLS > MAP NETWORK DRIVES # select a free drive letter ('X:' should be free now) # type in: " \\film-nas.med.ic.ac.uk\Scratch" into the folder address field # tick the box 'Reconnect at logon' and click OK # type in your username and password (on a microscope computer, use "ic\username" instead of just your username) The new FILM server should then automatically be mapped as 'drive X:' whenever you log in. Retrieving data from the old server The old server is not automatically mapped as drive X: anymore (which is actually pure coincidence, it got lost in a Windows update). If you still need to access the old server, just connect as described above, using '\\icfs19\imaging' as folder address. The old server will still be available as READ ONLY for a few weeks. If you have any problems, please ask for help. 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 00089] Fwd: Fwd: FW: PDRA position available (deadline 3rd August)
by Martin Spitaler 28 Jul '11

28 Jul '11

...forwarded for your information, Martin -------- Original Message -------- Subject: Fwd: FW: PDRA position available (deadline 3rd August) Date: Thu, 28 Jul 2011 09:35:40 +0100 From: Alex Sossick <ajs17(a)CAM.AC.UK> Reply-To: Alex Sossick <ajs17(a)CAM.AC.UK> To: <UK-EUROBIOIMAGING-PROJECT(a)JISCMAIL.AC.UK> ------------------------------------------------------------------------ *From:* Alessandro Esposito *Sent:* 28 July 2011 09:00 *To:* UK-EUROBIOIMAGING-PROJECT(a)JISCMAIL.AC.UK *Subject:* PDRA position available (deadline 3rd August) Dear all, I am looking for a post-doc that could support our research activities in the field of multidimensional time resolved detection. We have completed the construction of a new core imaging facility with two-photon, TCSPC, spectral, polarization capabilities. We are seeking to integrate new technologies in our system to push the boundaries of multidimensional imaging. You can find the call at the following URL: http://www.admin.cam.ac.uk/offices/hr/jobs/vacancies.cgi?job=8461 Information on our institute can be find here: http://www.hutchison-mrc.cam.ac.uk Information on my own research at the following website: http://www.quantitative-microscopy.org Please apply for the position as indicated in the call or contact me personally for further information (ae275(a)hutchison-mrc.cam.ac.uk <mailto:ae275@hutchison-mrc.cam.ac.uk>). The funding is limited in time to start with, but we are already looking for funding to extend this position. Apologies for the spam to the mailing list, but I thought it could be interesting for some of you. Kind regards, Dr Alessandro Esposito Senior Investigator Scientist MRC Cancer Cell Unit - Hutchison/MRC Research Centre Hills Road, CB20XZ, Cambridge (UK) +44(0)1223 331179 (office) +44(0)1223 763241 (FAX) +44(0)795 4383731 (mobile) The information in this email is confidential and may be legally privileged. It is intended solely for the addressee. If you receive this email by mistake, please notify the sender and delete it immediately. Opinions expressed are those of the individual and do not necessarily represent the opinion of Hutchison/MRC Research Centre. ------------------------------------------------------------------------ /The information in this email is confidential and may be legally privileged. It is intended solely for the addressee. If you receive this email by mistake, please notify the sender and delete it immediately. Opinions expressed are those of the individual and do not necessarily represent the opinion of Hutchison/MRC Research Centre./ -- UK-EUROBIOIMAGING Visit the website http://www.bioimaginguk.org To e-mail the group, send messages to UK-EUROBIOIMAGING-PROJECT(a)JISCMAIL.AC.UK To subscribe visit https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=UK-EUROBIOIMAGING-PROJECT --

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[FILM-Users 00088] Fwd: [1] new discussion on LinkedIn
by Martin Spitaler 22 Jul '11

22 Jul '11

...forwarded for your information, Martin -------- Original Message -------- Subject: [1] new discussion on LinkedIn Date: Thu, 21 Jul 2011 15:38:40 +0000 From: BioImagingUK Group Members <group-digests(a)linkedin.com> To: Martin Spitaler <m.spitaler(a)imperial.ac.uk> Linkedin Groups July 21, 2011 BioImagingUK Started by Sue Champion, Research Associate at University of Glasgow SINAPSE (Scottish Imaging Network: A Platform for Scientific Excellence) have a number of PhD studentships available to start in October... More Â» By Sue Champion, Research Associate at University of Glasgow

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[FILM-Users 00087] Fwd: Studentship for Imaging in Biomedical Research University of Sussex, UK
by Martin Spitaler 22 Jul '11

22 Jul '11

...forwarded, for your information, Martin Subject: Studentship for Imaging in Biomedical Research University of Sussex, UK From: Roger Phillips <[log in to unmask]> Reply-To: Confocal Microscopy List <[log in to unmask]> Date: Tue, 19 Jul 2011 15:57:48 +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 colleagues, I am Programme Convenor for the MSc in Imaging in Biomedical Research at the University of Sussex, Brighton, United Kingdom. Due to late withdrawals, we can still offer two fully funded (fees and stipend) MRC studentships for admission this October to our course. I would be very grateful if you would pass information about this opportunity on to your graduating students or other interested candidates. The programme includes taught and research components and covers various techniques in microscopy, medical imaging and image processing in equal parts. For further information and for application please follow the links: http://www.sussex.ac.uk/study/pg/2011/taught/1654/23871#tabs-1 http://www.sussex.ac.uk/study/pg/applying/ Please advise any interested student to contact me at R.G.Phillips(a)sussex.ac.uk Thanks for your help, Roger Dr Roger Guy Phillips Centre for Advanced Microscopy, University of Sussex School of Life Sciences John Maynard Smith Building Falmer, Brighton & Hove BN1 9QG United Kingdom phone:44 (0)1273 877585 fax: 44 (0)1273 678433 email: R.G.Phillips(a)sussex.ac.uk room:2C9 (ext 7585)/lab 4C2 (ext 2734)

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[FILM-Users 00086] OMERO: Version 4.3
by Martin Spitaler 22 Jul '11

22 Jul '11

Dear microscopists, the OMERO image database has now been upgraded to the new version OMERO 4.3 (thanks, Mark). This new version has some important new features: # IMPORT is now built into the main software (INSIGHT), so everything is now in one place # support for Volocity files from Widefield 1 (please report directly or let me know if you have any problems there), so all data from our facility microscopes are now supported (you can obviously also use it for non-facility images) # tagging at import # improved export (e.g. multiple files as OME-TIFF or JPG) # image registration (shift images by a number of pixels in XYZ) # create images and movies for publication For a full list of features and tutorials see <http://www.openmicroscopy.org/site/products/feature-list>. If you want to use the OMERO database, please get in contact with Mark Woodbridge from the Bioinformatics Support Service or myself. To use the latest version, simply always use the webstart link on <https://cisbic.bioinformatics.ic.ac.uk/cisbic/index.php/Imaging_Data_Manage…>. Just a note: It seems the server details got lost on upgrade, you might to re-add them the first time you start the new version. Simply click on the setup icon (top-right of the login window) and add <cell.bioinformatics.ic.ac.uk> as server. 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 00085] Fwd: Registration open now
by Martin Spitaler 20 Jul '11

20 Jul '11

...forwarded, for your information, Martin -------- Original Message -------- Subject: Registration open now Date: Wed, 20 Jul 2011 11:41:35 -0500 From: Definiens <symposium(a)definiens.com> Reply-To: <symposium(a)definiens.com> To: <m.spitaler(a)imperial.ac.uk> Definiens <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> Registration open now! *Definiens Symposium 2011* <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> Dear Martin Spitaler, After the great success and feedback from the Definiens Symposium 2010 <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> in Madrid, Definiens is pleased to announce the International Definiens Symposium 2011 <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…>. The venue will take place at the Moffitt Cancer Center in Tampa, Florida, October 17-18, 2011. We invite you to join this event to hear about groundbreaking research, meet other users and share your ideas. <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> The annual Definiens Symposium is the premier forum for Definiens users and developers from around the world to present their latest research, techniques and workflows in life science image and data analysis. Participants come from research institutions, bio-pharmaceutical companies and the healthcare sector. <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> *Venue:* Venue: H. Lee Moffitt Cancer Center and Research Institute, Vincent A. Stabile Research Building, 12902 Magnolia Drive, Tampa, FL 33612, USA The 2011 Definiens Symposium will be an ideal opportunity to share the latest ideas in state-of-the-art image analysis and to meet international experts from the Definiens community. Sessions <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> will include: * Biomarker Development and Validation * Basic Research and Drug Discovery * Toxicity and Efficacy Studies * Clinical Diagnostics A social networking event will take place in Tampa's latin quarter, Ybor City, on Monday evening. Transportation between the Symposium venue and the evening event will be arranged. We look forward to seeing you in Tampa. Regards, The Definiens Team *Definiens AG* Trappentreustrasse 1 80339 MÃ¼nchen Germany Tel. +49-89-231180-0 Contact Us <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> If you no longer wish to receive these emails, click on the following link: Unsubscribe <http://info.definiens.com/UnsubscribePage.html?mkt_unsubscribe=1&mkt_tok=3R…>

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[FILM-Users 00084] Fwd: Registration open now
by Martin Spitaler 20 Jul '11

20 Jul '11

...forwarded, for your information, Martin -------- Original Message -------- Subject: Registration open now Date: Wed, 20 Jul 2011 11:41:35 -0500 From: Definiens <symposium(a)definiens.com> Reply-To: <symposium(a)definiens.com> To: <m.spitaler(a)imperial.ac.uk> Definiens <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> Registration open now! *Definiens Symposium 2011* <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> Dear Martin Spitaler, After the great success and feedback from the Definiens Symposium 2010 <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> in Madrid, Definiens is pleased to announce the International Definiens Symposium 2011 <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…>. The venue will take place at the Moffitt Cancer Center in Tampa, Florida, October 17-18, 2011. We invite you to join this event to hear about groundbreaking research, meet other users and share your ideas. <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> The annual Definiens Symposium is the premier forum for Definiens users and developers from around the world to present their latest research, techniques and workflows in life science image and data analysis. Participants come from research institutions, bio-pharmaceutical companies and the healthcare sector. <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> *Venue:* Venue: H. Lee Moffitt Cancer Center and Research Institute, Vincent A. Stabile Research Building, 12902 Magnolia Drive, Tampa, FL 33612, USA The 2011 Definiens Symposium will be an ideal opportunity to share the latest ideas in state-of-the-art image analysis and to meet international experts from the Definiens community. Sessions <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> will include: * Biomarker Development and Validation * Basic Research and Drug Discovery * Toxicity and Efficacy Studies * Clinical Diagnostics A social networking event will take place in Tampa's latin quarter, Ybor City, on Monday evening. Transportation between the Symposium venue and the evening event will be arranged. We look forward to seeing you in Tampa. Regards, The Definiens Team *Definiens AG* Trappentreustrasse 1 80339 MÃ¼nchen Germany Tel. +49-89-231180-0 Contact Us <http://mkto-k0117.com/track?type=click&enid=bWFpbGluZ2lkPWRlZmluaWVuc0JldGF…> If you no longer wish to receive these emails, click on the following link: Unsubscribe <http://info.definiens.com/UnsubscribePage.html?mkt_unsubscribe=1&mkt_tok=3R…>

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[FILM-Users 00083] Fwd: [CISBIC-RA] hands-on light microscopy + modeling workshop
by Martin Spitaler 15 Jul '11

15 Jul '11

...forwarded, for your information, Martin -------- Original Message -------- Subject: [CISBIC-RA] hands-on light microscopy + modeling workshop Date: Thu, 14 Jul 2011 07:46:37 +0000 From: Endres, Robert G <r.endres(a)imperial.ac.uk> To: cisbic-announce <cisbic-announce(a)imperial.ac.uk>, cisbic-coi <cisbic-coi(a)imperial.ac.uk>, cisbic-news <cisbic-news(a)imperial.ac.uk>, cisbic-ra <cisbic-ra(a)imperial.ac.uk> Maybe you can also spread the word about our hands-on light microscopy + modeling workshop here in Bayreuth at the end of September (http://www.ep1.uni-bayreuth.de/weiss/de/courses/alm/index.html) We extended the deadline as we have still a few open slots for participants. Would you know interested PhD students or Postdocs in your or neighboring groups that would be interested to participate? The registration link is online under http://www.ep1.uni-bayreuth.de/weiss/de/courses/alm/registration Best Matthias Prof. Dr. Matthias Weiss Experimental Physics I University of Bayreuth Universitaetsstr. 30 D-95440 Bayreuth phone +49 921 55 2500 homepage: www.ep1.uni-bayreuth.de/weiss/en

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