- FILM-Users - imperial.ac.uk

[FILM-Users 00678] FW: Image analysis courses at the University of Cambridge and meeting request
by Gaboriau, David C A 07 Sep '16

07 Sep '16

Dear Users, Please see below for two courses on Image Analysis for Biologists at the University of Cambridge. I went last year and found the course very interesting and of very high quality. All the best, David From: UK Euro-BioImaging discussion list [mailto:UK-EUROBIOIMAGING-PROJECT@JISCMAIL.AC.UK] On Behalf Of Gabriella Rustici Sent: 06 September 2016 10:34 To: UK-EUROBIOIMAGING-PROJECT(a)JISCMAIL.AC.UK<mailto:UK-EUROBIOIMAGING-PROJECT@JISCMAIL.AC.UK> Subject: Image analysis courses at the University of Cambridge | December 2016 Dear All, Two bioinformatics course focusing on the analysis of imaging data will take place at the University of Cambridge in December 2016. Image Analysis for Biologists | Dec 12-14 This course will cover computational methods for analyzing cellular images and extracting quantitative data from them. Resources covered include Fiji, ImageJ and Icy. For more information on this event and details of how to register, visit: http://www.training.cam.ac.uk/bioinformatics/event/1879343 Using CellProfiler and CellProfiler Analyst to analyse biological images | Dec 15-16 This course will introduce users to the free open-source image analysis program CellProfiler<http://cellprofiler.org/> and its companion data exploration program CellProfiler Analyst. We will show how CellProfiler can be used to analyse a variety of types of imaging experiments. We will also briefly discuss the basic principles of supervised machine learning with CellProfiler Analyst in order to score complex and subtle phenotypes. For more information on this event and details of how to register, visit: http://www.training.cam.ac.uk/bioinformatics/event/1879361 Please note that these courses tend to book very quickly so I suggest registering early to avoid disappointment. Best regards, Gabry -- Gabriella Rustici, PhD Bioinformatics Training Manager Department of Genetics University of Cambridge Downing Street Cambridge CB2 3EH United Kingdom Email: gr231(a)cam.ac.uk<mailto:gr231@cam.ac.uk> Tel: +44 (0)1223 333614 URL: http://bioinfotraining.bio.cam.ac.uk/ -- UK-EUROBIOIMAGING Visit the website http://www.bioimaginguk.org To e-mail the group, send messages to UK-EUROBIOIMAGING-PROJECT(a)JISCMAIL.AC.UK<mailto:UK-EUROBIOIMAGING-PROJECT@JISCMAIL.AC.UK> To subscribe visit https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=UK-EUROBIOIMAGING-PROJECT --

1 0

[FILM-Users 00677] FW: Disruption if working in SAF this weekend
by Rothery, Stephen M 02 Sep '16

02 Sep '16

From: Wigley, Fraser Sent: 02 September 2016 11:42 To: Building, Sir Alexander Fleming <est-sir-alexander-fleming-building-dl(a)imperial.ac.uk> Cc: St Clair Laing, Michael A <m.stclair(a)imperial.ac.uk> Subject: Disruption if working in SAF this weekend Dear All, If you plan to work in the Sir Alexander Fleming building this weekend (3-4 September), please be aware of the following disruption: * There will be no hot water from 8am to 8pm on Saturday * There will be no steam supply from 6pm today (Friday) until 6pm on Sunday * There will be no access through the lobby outside the security reception and post room on the ground floor from 8am to 4pm on Saturday, whilst the floor is repaired. Please use the main lifts instead of the lifts in the northeast corner. There will be further disruption to the hot water and steam next weekend - more details nearer the time. Regards, Fraser Fraser Wigley Building Manager RCS1 | Sir Alexander Fleming | Chemistry | Sir Ernst Chain | Flowers www.imperial.ac.uk/people/f.wigley<http://www.imperial.ac.uk/people/f.wigley>

1 0

[FILM-Users 00676] Post-doc position in Strasbourg
by Gaboriau, David C A 30 Aug '16

30 Aug '16

Dear Users, Please find attached a Post-doc offer in Strasbourg to study platelet formation by intravital imaging. All the best, David From: gdr2588-request(a)services.cnrs.fr [mailto:gdr2588-request@services.cnrs.fr] On Behalf Of Basile GURCHENKOV Sent: 30 August 2016 10:44 To: gdr2588(a)services.cnrs.fr Subject: [GDR2588-MIV] offre Post-doc Strasbourg Decription ci-jointe.

1 0

[FILM-Users 00675] F!!!!!!!!!!!!!!!!!!!!!!!! Deletion of scratch files !!!!!!!!!!!!!!!!!!!!!!!!!!!!
by Rothery, Stephen M 19 Aug '16

19 Aug '16

Dear All We need to delete older files from scratch Please make sure you have copied all older files off All data from before the 1st June will be deleted on Monday Bw Steve FILM - Facility for Imaging by Light Microscopy ************************************************************** Steve Rothery FILM Technician Sir Alexander Fleming Building, desk 403 Imperial College London / South Kensington Exhibition Road London SW7 2AZ Tel +44-(0)207 594 9793 And ICTEM, (L-Block) Room 314 Hammersmith Campus Imperial College London Du Cane Road London, W12 0NN Tel. +44-(0)207 594 1669 E-mail s.rothery(a)imperial.ac.uk<mailto:s.rothery@imperial.ac.uk> Website: http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ **************************************************************

1 0

[FILM-Users 00674] Nikon educational workshop at FILM
by Gaboriau, David C A 19 Aug '16

19 Aug '16

Dear Users, We are organising a microscopy workshop with Nikon at FILM, in the last week of November (24th-30th). The programme is in preparation, but the week would possibly include: * Seminar on the Nikon software JOBS, super-resolution techniques... * Hands-on sessions on the widefield/confocal High-Content system at FILM using JOBS with Advanced Imaging Specialists. * A demo of a new super-resolution system, the VisiTech iSIM (http://www.visitech.co.uk/vt-isim.html) The idea is that Users could bring some samples and book time slots on these microscopes, with the help of the Imaging Specialists. Would it be possible to let us know if that could be of interest to you? All the best, David David Gaboriau, PhD FILM - Facility for Imaging by Light Microscopy High-Content Microscopy Specialist Sir Alexander Fleming Building, desk 408 Imperial College London / South Kensington Exhibition Road London SW7 2AZ, UK Phone: +44 (0)2075 949 793 Email: d.gaboriau(a)imperial.ac.uk<mailto:d.gaboriau@imperial.ac.uk> Website: http://imperial.ac.uk/imagingfacility

1 0

[FILM-Users 00673] Fw: [lsr-group] Post-doc position - Quantitative live cell imaging of cell decision-making
by Gaboriau, David C A 16 Aug '16

16 Aug '16

Dear Users, Please see below for a Post-Doc position at UCL. Best, David ________________________________ From: lsr-group-bounces(a)imperial.ac.uk <lsr-group-bounces(a)imperial.ac.uk> on behalf of Ricardo Henriques <r.henriques(a)ucl.ac.uk> Sent: 16 August 2016 11:03 To: lsr-group Cc: Jonathan Subject: [lsr-group] Post-doc position - Quantitative live cell imaging of cell decision-making Dear all, The Chubb lab at UCL is currently looking for a post-doc. They're doing exciting research - http://www.ucl.ac.uk/lmcb/users/jonathan-chubb. Jonathan Chubb | LMCB - MRC Laboratory for Molecular Cell ...<http://www.ucl.ac.uk/lmcb/users/jonathan-chubb> www.ucl.ac.uk Gene expression dynamics. Despite the generation of transcriptional differences between nearby related cells being the basis of most differentiation and disease, our ... Announcement attached below. All the best, -Ricardo -- Ricardo Henriques, PhD http://www.ucl.ac.uk/lmcb/research-group/ricardo-henriques-research-group MRC-Laboratory for Molecular Cell Biology University College London Gower Street London WC1E 6BT United Kingdom

1 0

[FILM-Users 00672] Data Scientist Vacancy in CLF OCTOPUS Facility
by Rothery, Stephen M 11 Aug '16

11 Aug '16

From: Rolfe, Daniel (STFC,RAL,CLF) Sent: 11 August 2016 09:31 To: RCaH Everyone Subject: Data Scientist Vacancy in CLF OCTOPUS Facility Dear all, We are looking for an experienced data analysis algorithm developer/researcher interested in applying their skills to biological imaging and cancer research as part of a multidisciplinary team in the CLF's OCTOPUS facility here in the Research Complex at Harwell. Full details are here - http://www.topcareer.jobs/Vacancy/irc229651_6616.aspx The closing date is 29 August. For more information please contact me. I'd be very grateful if you could share this with any colleagues who you think might be interested or who might know possible candidates. Many thanks, Dan FILM - Facility for Imaging by Light Microscopy ************************************************************** Steve Rothery FILM Technician Sir Alexander Fleming Building, desk 403 Imperial College London / South Kensington Exhibition Road London SW7 2AZ Tel +44-(0)207 594 9793 And ICTEM, (L-Block) Room 314 Hammersmith Campus Imperial College London Du Cane Road London, W12 0NN Tel. +44-(0)207 594 1669 E-mail s.rothery(a)imperial.ac.uk<mailto:s.rothery@imperial.ac.uk> Website: http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ **************************************************************

1 0

[FILM-Users 00671] Job Opportunity: postdoc to work between the Nikon Imaging Centre and EM facility at King’s
by Rothery, Stephen M 11 Aug '16

11 Aug '16

Hi all, We’re hiring a postdoc to work between the Nikon Imaging Centre and EM facility at King’s. Details are at: https://www.hirewire.co.uk/HE/1061247/MS_JobDetails.aspx?JobID=71839 Please forward onto anyone else that might be keen. Cheers, Maddy ************************************************************* Maddy Parsons, PhD Professor of Cell Biology, Director: Nikon Imaging Centre@King’s Kings College London, Randall Division of Cell and Molecular Biophysics Room 3.22B, New Hunts House, Guys Campus, London, SE1 1UL UK Tel: +44 (0)207 848 8164 Fax: +44 (0)207 848 6435 Email: maddy.parsons(a)kcl.ac.uk<mailto:maddy.parsons@kcl.ac.uk> http://www.kcl.ac.uk/lsm/research/divisions/randall/research/sections/motil… http://nic.kcl.ac.uk/ ************************************************************* FILM - Facility for Imaging by Light Microscopy ************************************************************** Steve Rothery FILM Technician Sir Alexander Fleming Building, desk 403 Imperial College London / South Kensington Exhibition Road London SW7 2AZ Tel +44-(0)207 594 9793 And ICTEM, (L-Block) Room 314 Hammersmith Campus Imperial College London Du Cane Road London, W12 0NN Tel. +44-(0)207 594 1669 E-mail s.rothery(a)imperial.ac.uk<mailto:s.rothery@imperial.ac.uk> Website: http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ **************************************************************

1 0

[FILM-Users 00670] !!!!!!!!!!!!!!!!!!!!!!!! Deletion of scratch files !!!!!!!!!!!!!!!!!!!!!!!!!!!!
by Rothery, Stephen M 05 Aug '16

05 Aug '16

We need to delete older files from scratch Please make sure you have copied all older files off All data from before the 1st May will be deleted Bw Steve FILM - Facility for Imaging by Light Microscopy ************************************************************** Steve Rothery FILM Technician Sir Alexander Fleming Building, desk 403 Imperial College London / South Kensington Exhibition Road London SW7 2AZ Tel +44-(0)207 594 9793 And ICTEM, (L-Block) Room 314 Hammersmith Campus Imperial College London Du Cane Road London, W12 0NN Tel. +44-(0)207 594 1669 E-mail s.rothery(a)imperial.ac.uk<mailto:s.rothery@imperial.ac.uk> Website: http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ **************************************************************

1 0

[FILM-Users 00669] FW: security vulnerability in OMERO - news
by Rothery, Stephen M 03 Aug '16

03 Aug '16

For anyone using the 0mero data system From: Butcher, Sarah A Sent: 03 August 2016 10:07 To: Magee, Tony Subject: security vulnerability in OMERO - news Dear Prof Magee The OMERO team have just released details of a serious security issue with OMERO server as below: http://www.openmicroscopy.org/site/products/omero/secvuln/2016-SV2-share Improper Access Control Vulnerability. The OMERO.shares system bypasses intended security restrictions and grants elevated privileges to read otherwise-restricted data. A user can retrieve data belonging to users across all groups by using the API. The user must be able to authenticate remotely using the standard 4063 and 4064 ports and have exploit code to make use of the vulnerability. There are several things we can do to mitigate this issue but all will effect some aspects of OMERO functionality for the medium term. We are only seeing about 12 logins a month on OMERO but there is quite a lot of data associated with it, including a number of 'shares' belonging to FILM. The security issue affects the share function and their patch scripts simply dump all active shares and stop new ones being created. All information regarding the current shares will be removed by the 'patch', and while we can keep a snapshot of the current version of the database as a record, direct merging of any shares information in that with new data accumulated subsequent to the patch, in a new version will not be possible. This does not mean that images will be deleted, but it does mean that lists of people who can access specific 'shared' datasets will be lost, along with shared access. We currently have a number of shares in our OMERO deployment and FILM are associated with some of them - there is also a 'public' share but the OMERO code does not make it all easy to see who may be using the public share. If we remove the 'shares' function by using the patch, it will not be re-instated until we move to a completely new version of OMERO. I do not have a timeline for this at present as they have dropped support for the current Red Hat release and we will have to set up a completely new system in a new VM with a different OS on a different server, which will require extensive testing. We will do this, but not until later in the year when a number of other big infrastructure upgrades are further down the line. In order to exploit the vulnerability a user has to access the named ports via the API. We have instigated a less draconian workaround that also protects against this vulnerability as follows: We have disabled all access to the Java client - access is normal via the web interface. The vulnerable ports are now blocked. This combination stops the necessary access for the exploit. I would like to send an update to users via the FILM mailing list later today but wanted to let you know the situation first. I have also informed Paul French as his group are heavy users. If the java client is absolutely required, we will have to apply the patch which will remove all shares instead. I am in today and tomorrow and I will be available to talk about this until Saturday, when I go on leave until the 22nd August. I am not sure who to send a message for the FILM list to at present? Best wishes Sarah -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-. Dr Sarah Butcher Head, Bioinformatics Data Science Group (BDSG) Please note new group name, department and location: Room 129, Sir Alexander Fleming Building Department of Surgery and Cancer Faculty of Medicine South Kensington Campus Imperial College London SW72AZ +44 (0)20 759 45734 www.imperial.ac.uk/bioinfsupport<http://www.imperial.ac.uk/bioinfsupport> -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-

1 0