- FILM-Users - imperial.ac.uk

[FILM-Users 00913] FILM-news
by Bruckbauer, Andreas 03 Aug '20

03 Aug '20

Dear FILM-users, Some updates about the facility: * We have successfully trialled microscopy user-trainings using a combination of socially distanced on-site induction (with face masks) and remote assistance with screen sharing and want to offer this now to potential new users. Please understand that it might be more difficult to have staff available due to COVID-19 restrictions, so there will be a waiting list. * Currently only one of the widefield microscopes in room SAF 409 can be used due to COVID-19 restrictions, we plan to move the WF3 microscope next door, to room 410, so that both microscopes can be used at the same time. * We have deactivated the forms on the widefield microscopes as this did not work with our booking restrictions, please let us know if you need a special objective or filter-set well in advance. * Please wear face masks if you can. * Alice, who has done an excellent job as parental leave cover for David, has now left FILM as her contract came to the end. Thanks Alice! Best wishes and successful imaging! The FILM team ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ SAF 4th floor, open space desk 401 +44 (0)20 7594 2023 a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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[FILM-Users 00912] SAF building access
by Bruckbauer, Andreas 20 Jul '20

20 Jul '20

Dear FILM-users, Please be aware that the College is still operating under 'College closure' conditions which require Head of Department approval for access to buildings, all access from before the shutdown has been wiped. Access is currently granted on a building-by-building level. When you are not usually based e.g. at the SAF building, you won't automatically get access to this building, even if you have access to other buildings. To grant you access to the building, we need an email from your Head of Department who authorizes your access. For some departments this is delegated to an administrator. Please don't wait with yourCOVID-19 induction for the FILM facility until the last minute only to find out that you don't have access yet. Best wishes Andreas ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ SAF 4th floor, open space desk 401 +44 (0)20 7594 2023 a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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[FILM-Users 00911] Face coverings in microscope rooms
by Bruckbauer, Andreas 13 Jul '20

13 Jul '20

Dear FILM-users, We would like to encourage microscope users to wear face coverings in the FILM facility. This is additional to the main COVID-19 control measures such as cleaning and social distancing which need to be observed at all times. The face coverings might allow some additional protection when the 2 m distance rule cannot be adhered to for brief times, e.g. FILM staff entering a microscopy room to retrieve tools or samples. Stay safe and good luck with your imaging projects! Andreas ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ SAF 4th floor, open space desk 401 +44 (0)20 7594 2023 a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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[FILM-Users 00909] FILM support
by Bruckbauer, Andreas 23 Jun '20

23 Jun '20

Dear all, I am on annual leave and will be back on July 3rd, if you are doing essential work and need support with the microscopes, please contact Stephen Rothery or David Gaboriau. Best wishes Andreas ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ SAF 4th floor, open space desk 401 +44 (0)20 7594 2023 a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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[FILM-Users 00908] FW: [lsr-group] Postdoc positions in our lab
by Bruckbauer, Andreas 12 Jun '20

12 Jun '20

FYI: Postdoc positions in Portugal From: lsr-group-bounces(a)imperial.ac.uk <lsr-group-bounces(a)imperial.ac.uk> On Behalf Of Ricardo Henriques Sent: 12 June 2020 16:44 To: lsr-group <lsr-group(a)imperial.ac.uk> Subject: [lsr-group] Postdoc positions in our lab This email from r.henriques(a)ucl.ac.uk<mailto:r.henriques@ucl.ac.uk> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Hi everyone, A small favour to ask. We have a couple of positions open for researchers with a strong background in Microscopy, to be hosted in our new lab at Instituto Gulbenkian de Ciência (Portugal). These are for: - Postdoctoral Researcher: Viral Host-Pathogen Interactions and Cell Biology - Postdoctoral Researcher: Optical and Computational Biophysics Info in: https://henriqueslab.github.io/positions/ Can you pass please disseminate these to anyone that may be interested. Thank you in advance. Hope you're staying safe. All the best, -Ricardo -- Prof. Ricardo Henriques, Chair of Computational and Optical Biophysics University College London and Francis Crick Institute [https://drive.google.com/uc?id=1IC7xLHfcTBc1L3IB9fGOznFsFiGUJ4Ib&export=dow…] MRC-Laboratory for Molecular Cell Biology University College London Gower Street London WC1E 6BT United Kingdom Twitter: @HenriquesLab<https://twitter.com/HenriquesLab> Website: https://henriqueslab.github.io<https://henriqueslab.github.io/> Google Scholar: https://scholar.google.co.uk/citations?user=-peQ4ZsAAAAJ&hl=en Co-Director of the Wellcome Trust Optical Biology<https://opticalbiology.org/> PhD programme

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[FILM-Users 00907] Partial re-start of FILM from Wednesday 03/06/2020
by Bruckbauer, Andreas 29 May '20

29 May '20

Dear FILM-users, We plan to re-start operations in the FILM facility from Wednesday 03/06/2020, as mentioned earlier, there will be new rules in place to operate the microscopes safely, please find the current version attached to this email. These rules might change as the situation evolves and we will issue updates, please ask FILM staff if you are unsure. Before using the facility, all users need to have an additional induction to familiarize themselves with these rules, this can be done with a FILM member remotely. First logon to PPMS where you will be presented with this document, after agreeing to it online, request a COVID-19 rules induction on PPMS. [cid:image002.jpg@01D635DD.E1F23600] If you experience problems send an email to: film-service(a)imperial.ac.uk<mailto:film-service@imperial.ac.uk> Important: College buildings are only partial reopening for work that cannot be done at home, special permission is required for access, if you do not already have this permission for our building, then we need authorisation from your head of department to request building access. Best wishes Andreas, Steve, David and Alice ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ SAF 4th floor, open space desk 401 +44 (0)20 7594 2023 a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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[FILM-Users 00906] Preparations for using the FILM-facility during COVID-19
by Bruckbauer, Andreas 18 May '20

18 May '20

(apologies if you receive this email more than once) Dear FILM-users, As stated in the Imperial COVID-19 updates, the campuses remain closed and everyone should continue to stay/work at home. But we start to prepare for partial re-opening of the FILM facility at some point in the future and in line with Government, College and NHLI guidelines as well as advice from the international imaging community. The way we can operate will depend on many factors, including the situation on public and private transport for FILM staff to come into work. We anticipate that availability of staff and microscopes will be greatly reduced when we re-open the facility and ask our users to consider this when planning experiments. Based on social-distancing guidelines, we have drafted the following rules which might change as this is a fast moving situation, but I wanted to share them with you now: FILM is shared by users from different research groups and departments which causes a higher risk for SARS-CoV-2 transmission and works against controlling the spread of potential new outbreaks. Therefore, it is important that additional care is taken when working in the facility. Before using the facility again, all users need to have an additional induction to familiarise themselves with these rules, this can be done remotely with a FILM member (please wait for this until you really need to use the microscope as the rules might change). Social distancing Objective: To maintain 2m social distancing at the microscopes, including while arriving at and departing from the facility, and when travelling between sites. * Microscope users including staff must keep 2 metres apart. * All microscope usage must be booked in advance. * Only one user is allowed at the microscope at a time. * In small rooms (SAFB 409, XXX), only one microscope can be used at a time, this is enforced through the booking system and clearly signposted at the door. * In larger rooms (408, XXX) with multiple microscopes extra care must be taken and users need to cooperate to comply with the 2 m distance rule (Floor markings will guide users to comply with the rule - to be installed). * There is now a minimum time of 30 min between bookings to allow air-exchange in the room between users, this is enforced by the booking system. * The analysis computers are to be used remotely. * In an emergency, for example, a chemical spill or fire, people do not have to stay 2m apart if it would be unsafe. Handwashing and Cleaning Objective: To keep the workplace clean and prevent transmission by touching contaminated surfaces. * Wash your hands frequently, at least at the start and end of the session. In rooms where there is not hand wash basin (SAFB 408, 409, 527, ICTEM L-Block 314), we will supply hand sanitiser. * Avoid touching your face and cough or sneeze into your arm, do not come to work if you have COVID-19 symptoms. https://www.nhs.uk/conditions/coronavirus-covid-19/check-if-you-have-corona… * The user must clean the parts of the microscope which are touched during operation regularly with 70% ethanol. These are e.g. focus knobs, eyepieces, sample holder, immersion oil bottle, touchpad, computer keyboard and mouse. Keyboard, mice and microscope eye pieces will be covered in cling film and additional cling film supplied for regular replacements. Spray ethanol on tissue and wipe the parts or the cling film covering them. Dispose of tissues and film in clinical waste baskets. * The use of lab coats and face masks is as required by the experiment before COVID-19 but restricted to single use lab coats only. * Staff and users wear surgical facemasks when in close proximity to each other and when this cannot be avoided. Staff availability and training * According to the guidance, staff will work from home as much as possible and only come into the facility if remote help is not possible. We also anticipate that using public transport will be difficult and this will impact on our availability on site. * All user trainings are currently suspended because it would currently be impossible to adhere to the 2m distance rule and trainings take too long to rely on face masks for protection. This applies until we have implemented options for remote training. Best wishes Andreas ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ SAF 4th floor, open space desk 401 +44 (0)20 7594 2023 a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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[FILM-Users 00905] Free bioimage analysis online courses NEUBIAS Academy
by Spenlehauer, Alice H M 06 Apr '20

06 Apr '20

The network of European bioimage analysts (NEUBIAS) Academy is offering free online courses and webinars - https://neubiasacademy.org (see more details in email thread below). Of particular interest, next week on April 14th and 15th there will be two live sessions on the basics of macro creation and scripting in ImageJ/FIJI (register here<https://docs.google.com/forms/d/e/1FAIpQLSdieqTNlxez7VEZN0KW7a9XHAaN1quT-nk…>). This could be a good opportunity for users who want to learn how to: (1) automate and speed up their image analysis workflows; and (2) make their image analysis more reproducible. For those who are interested but unable to attend, NEUBIAS will be recording the course and will be releasing it on the NEUBIAS youtube channel for further viewing. I hope that everyone is keeping healthy. Best Wishes, Alice From: Image Analysis Focused Interest Group of the Royal Microscopical Society <IAFIG-RMS(a)JISCMAIL.AC.UK<mailto:IAFIG-RMS@JISCMAIL.AC.UK>> On Behalf Of Dominic Waithe Sent: 03 April 2020 17:21 To: IAFIG-RMS(a)JISCMAIL.AC.UK<mailto:IAFIG-RMS@JISCMAIL.AC.UK> Subject: [IAFIG] Announcement: Opening of the NEUBIAS Academy This email from dominic.waithe(a)IMM.OX.AC.UK<mailto:dominic.waithe@IMM.OX.AC.UK> originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> to disable email stamping for this address. Dear Bioimaging colleagues, We are thrilled to announce the Opening of the NEUBIAS Academy https://neubiasacademy.org NEUBIAS Academy is a new initiative, aimed to provide sustainable material and activities focused on Training in Bioimage Analysis. NEUBIAS Academy capitalizes on the success of NEUBIAS’ 15 Training Schools (2016-2020) that have supported over 400 trainees (Early Career Scientists, Facility Staff and Bioimage Analysts), but could not satisfy the high and increasing demand (almost 1000 applicants). A team of about 20 members will interact with a larger pool of hundreds of trainers, analysts and developers to bring knowledge and bleeding-edge updates to the community. Where do we start? NEUBIAS Academy @ Home: Online events NEUBIAS aims to support the community with a new series of live online events targeting all levels of Bioimage Analysis Technology, with intensive activity to best serve the community during the currently challenging period of confinement: - Live Online Courses will provide interactivity with the audience (e.g. exercises in virtual breakout rooms), - Live Webinars will target a larger audience with specific topics, software tools, theoretical content or critical updates, from introductions to concepts to very advanced implementations. Questions and Answers will be moderated by experts. Webinars will be recorded and made available on Youtube NEUBIAS Channel, and a thread per event will be opened in the image.sc Forum to report Q&As and to welcome further questions/comments. Starting list of confirmed events: 14-15 April: IJ/Fiji Macro Programming, online course. open for Registration ! 21 April: Introduction to Machine Learning and DeepImageJ open for Registration ! 22 April: Bioimage Analysis with Icy open for Registration ! 29 April: Quantitative Pathology and Bioimage Analysis: QuPath v0.2.0 30 April: Advanced Image Processing with MorphoLibJ You’ll find more information on https://neubiasacademy.org Please spread the word On behalf of the NEUBIAS Academy organisation committee ________________________________ To unsubscribe from the IAFIG-RMS list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=IAFIG-RMS&A=1

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[FILM-Users 00904] Tutorial: Guidance for quantitative confocal microscopy
by Bruckbauer, Andreas 01 Apr '20

01 Apr '20

Dear all, I want to highlight the excellent paper by James Jonkman et al. Tutorial: Guidance for quantitative confocal microscopy published yesterday in Nature Protocols: https://www.nature.com/articles/s41596-020-0313-9 It is a very comprehensive guide for confocal microscopy including sample preparation, instrumentation, image acquisition and even statistics, maybe the best ever written on this topic! Please read before using the FILM microscopes, we also included a link on our webpage under Resources/General Information. Best wishes Andreas ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ SAF 4th floor, open space desk 401 +44 (0)20 7594 2023 a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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[FILM-Users 00903] FILM image analysis help during college closure
by Bruckbauer, Andreas 23 Mar '20

23 Mar '20

Dear FILM-users, We hope you are all safe and well and able to work remotely. The film team is adjusting to this new way of working and we already got a number of requests from users who are writing up results. We will continue to give advice on image analysis - for help connecting to scratch see at the end - - For simple questions, just continue to send an email either to one of us or to film-service(a)imperial.ac.uk<mailto:film-service@imperial.ac.uk> - If you want a bit more help, please request 'Remote Help with Image Analysis<https://ppms.eu/imperial/req/?pf=2&training=true&form=71>' on our PPMS booking system under 'requests, this allows us to distribute requests to the members of the FILM team and process a queue of requests in the order they come in. Please also indicate the location of an example image on our scratch2 server. - We might need to charge staff assistance (£29 / hour) for image analysis help, but plan to keep the first two hours free of charge for data acquired using our microscopes. The facility charges, including a large part of our salaries, are recovered from the microscope usage charges, when the microscopes are not booked, the facility has no income. - Image analysis help could be done as step-by-step guides sent via e-mail and/or or additional telephone sessions. When screen sharing is necessary, Skype, Zoom or maybe Microsoft teams might be possible, but this will depend on the user's and team member's individual preferences and we have to experiment a bit with these. - FILM has four remote desktop workstations with powerful processors and lots of RAM, one of them runs the Huygens deconvolution software. They all have Fiji installed, this might be an option if you have larger files which you cannot analyze with your own computer. However the graphic cards on these machines have some limitations, they are not suitable for 3D rendering, please ask FILM for access and further details. - The Royal Microscopical Society has set up a web page for online resources: https://www.rms.org.uk/study-read/news-listing-page/online-microscopy-talks… Connecting to scratch from home: When you are not on the college network, you would need to use a VPN connection to connect your home computer directly to scratch, use IC\username (your own user name) to connect. See ICT webpages on how to connect to a VPN: https://www.imperial.ac.uk/admin-services/ict/self-service/connect-communic… Another option is to remotely connect to your college computer (if you have one), this should work without VPN, when the windows remote desktop is configured correctly as described here: https://www.imperial.ac.uk/admin-services/ict/self-service/connect-communic…. You might need to wake up the computer first, but ICT has ICT have turned off 'power save mode' so your work PC will not go to sleep while you are working remotely if you needed to leave it running. You might be able to copy and paste files from the remote connection directly to your home PC (this might take a while) or save to e.g. your One Drive. The file exchange is a way to send large files to collaborators: https://www.imperial.ac.uk/medicine/study/e-learning/blackboard-access-and-… All the best! Andreas, Steve and Alice ---------------------------------------------------- Dr Andreas Bruckbauer FILM facility manager Sir Alexander Fleming Building South Kensington Campus Imperial College London Exhibition Road London, SW7 2AZ Working remotely from home a.bruckbauer(a)imperial.ac.uk<mailto:a.bruckbauer@imperial.ac.uk> http://www.imperial.ac.uk/medicine/facility-for-imaging-by-light-microscopy/ ----------------------------------------------------

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