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Revision as of 10:55, 2 February 2010

Following up the successful meetings in York (2008) and Manchester (2009), the next Microscopy Facility Manager Meeting will be in London, at Imperial College, in January 2010.

Summary and outcome

Shortly, summaries of the meeting and the several break-out sessions will be added here.

The break-out sessions will feed directly into the BioimagingUK working groups, for the latest updates see the respective subpages of BioimagingUK

Training

Summary to come soon

High-Throughput Microscopy

Summary to come soon; see also working group Higher speed/content/throughput functional imaging

In Vivo Imaging

Tools for in vivo imaging

Chair: Paul Thomas, Univ. East Anglia

Also present at the break-out session: Ben Atkinson, Intelligent Imaging; Grant Calder, John Innes Centre; Dave Clarke, Rutherford Appleton Laboratory, STFC; Paul Cormack, Hamamatsu Photonics UK Ltd.; Ana-Maria Calcagno-Pizarelli, Imperial College London; Roy Edward, Biostatus Ltd; Felicity Gavins, Imperial College London; Trudi Gillespie, Univ. Edinburgh; Colin Gray, Univ. Sheffield; Peter Humphreys, WT Centre for Stem Cell Research Cambridge; Peter Jordan, CRUK London; Emma King, Univ. Dundee; James McKechnie, Media Cybernetics UK; Luis Pizarro, Imperial College London; Kees Straatman, Univ. Leicester; Rolly Wiegand, Univ. Edinburgh.

A small group (listed above) met to discuss the use and development of tools for more physiological (in vivo) imaging. The break-out session was followed by a round-table discussion involving all the meeting attendees. Below are the major points that arose out of both the break-out session and the subsequent summary session:

General in vivo imaging

• The need for a central facility providing access to all UK scientists was a major discussion point. Overall it was felt that there are already a large number of facilities across the UK which provided sufficient access to external scientists; and thus, a central facility didn’t make much sense.

• Nevertheless, it was felt that the availability and accessibility of in vivo imaging facilities might be better advertised; perhaps, through the UK LM facility website.

• Furthermore, it was also thought that the UK LM facility website could indicate which facility managers were willing to provide help and advice (applies to other areas of expertise as well as in vivo).

• Even considering the fact that the majority didn’t support the idea of a central facility, it was acknowledged that one disadvantage of local in vivo imaging is that in vivo and standard microscopy can often exclude each other; thus, causing duplication of equipment.

• It was also felt that centres of excellence dedicated to specialized forms of in vivo imaging (similar to the centres established by the Scottish Universities Life Sciences Alliance; SULSA) might be a good idea. The major advantage of the SULSA model being the equal charges and accessibility applied to all investigators; thus, providing facilities for those scientists at institutes that have no in vivo capability.

• Another major point of contention was the problem of Home Office licensing. There was overall dissatisfaction with the inconsistency of different Home Office inspectors in applying the same rules in different ways. Likewise, there was a feeling that licences were overly restrictive; the fact that a licence is linked both to an experiment and a location was a big problem. If the Home Office would change it so an experiment could be done in any licensed premises, that would help.

Cat-3-specific points

• Unlike general in vivo imaging, it was felt that a central facility for Cat 3 work is needed; perhaps, at site that has most safety procedures already in place – e.g., Pirbright (animals) and Rothamsted (plants).

• However, it was pointed out that a Cat 3 licence is always specific for an organism, two Cat 3 experiments can’t necessarily share the same space, leading to duplication of equipment.

See also working group In Vivo Imaging

Funding and Sustainability

Summary to come soon; see also working group Sustainability

Software and Data

Chair: Paul Thomas, Univ. East Anglia

Also present at the break-out session: Ben Atkinson, Intelligent Imaging; Grant Calder, John Innes Centre; Colin Gray, Univ. Sheffield; Ki Hng, MRC Clinical Sciences Centre; Deliza Ibanez-Garcia, Bitplane AG; James McKechnie, Media Cybernetics UK; Anton Page, Univ. Southampton; Luis Pizarro, Imperial College London; Tim Self, Univ. Nottingham; Alex Sossick, Univ. Cambridge; Kees Straatman, Univ. Leicester; Simon Walker, Babraham Institute.

The small group (listed above) met to discuss the use and development of software tools for data management, archiving and analysis. The break-out session was followed by a round-table discussion involving all the meeting attendees. Below are the major points that arose out of both the break-out session and the subsequent summary session:

• The Facility managers overwhelmingly supported moving to a single, standardized file format (e.g., OME-TIFF). This idea was also tentatively supported by representatives of companies developing image-analysis software. Nevertheless, it was thought that a stumbling block would be the acceptance of this idea by image-acquisition companies.

• One objection raised by imaging software developers was that the present OME-TIFF format does not encompass all the necessary meta-data.

• There was general support for an on-line, centralised database for published images that includes all original images generated in support of a publication (similar to the JCB DataViewer, but global).

• It was thought that such a database would be useful for validation of data by peers, and would also enable software developers to check new algorithms on “standard” datasets.

• There was less enthusiasm demonstrated for the adoption of the OME database (Omero). In the past, some managers had tried Omero, but had failed to get it to work. These managers were disinclined to try again with the newer version despite assurances from managers with newer installations that it was now much improved.

• Those managers using Omero argued that it enabled better organisation of large amounts of data, and simpler access to archived images.

• The majority of managers were not users of Omero – perhaps, the biggest impetus to uptake will come if the centralised database is implemented forcing imagers to seriously consider archiving their data in an easily searchable and accessible repository.

• Additional impetus for implementation of Omero (or something similar) may also come from funders that begin to seriously apply their rules regarding data archiving and access.

• Those who use Omero (as well as those who had tried) felt that uptake of Omero might be greater if it was simpler to install and had more image analysis tools.

• One of the problems identified with Omero is the data duplication problem where data is kept in its original format and as OME-TIFF in the Omero database, increasing the data storage required for data and backups.

• There was much discussion of commercial alternatives to Omero (e.g., Imagik). The general feeling was that there could be problems of data retrieval if the company were to collapse, or if users were no longer able to afford the service. It was thought that this was less of a problem with open-source software such as Omero.

• A separate issue was how, and to what degree, can experimental (as opposed to image) meta-data be standardised and saved along with the images (e.g., sample preparation, organism, tissue, etc.)

• Many managers thought that more workshops aimed at software training would be useful; especially, for open-source software (ImageJ, Omero, µManager). Although, it was pointed out that RMS runs image processing workshops every year (June) – and these include ImageJ.

• Idea for next year’s meeting: Omero workshop.

See also working group Software Tools & Data Management

High-Resolution Microscopy

Summary to come soon; see also working group Higher Spatial Resolution

Careers

Summary to come soon; see also working group Careers

Programme

=> volunteers to chair break-out sessions needed!

=> feedback is still very welcome! (m.spitaler@imperial.ac.uk)

Thursday 7 January 2010

• 12.00-13.00 Arrival, sandwich lunch and registration for break-out sessions
• 13.00-13.15 Welcome, latest updates on programme
• 13.15-13.30 Introduction of participants
• 13.30-14.15 Short reports & discussions
  • Paul Thomas, UEA: Multiphoton microscopes
  • Peter Humphreys: STJ detectors
  • ad hoc topics

• 14.15-14.45 Technical Report: James Francis (MediaCybernetics): "How to quantitatively test and compare cameras" (the practical demonstration announced previously has been snowed in and is cancelled)

• 14.45-15.15 coffee

• 15.15-15.30 Update BioimagingUK / Eurobioimaging
• 15.30-15.45 Introduction Break-out Sessions I (chaired by...):
  • Training (Yan Gu)
  • High-throughput microscopy (Nick Barry)
  • In vivo imaging (Peter O’Toole)
  • Funding & sustainability (Lucy Collinson)
• 15.45-17.00 Break-out sessions I
• 17.00-18.00 Summary of break-out sessions by session leaders, discussion
• 18.00-19.00 hotel check-in
• 19.00-late dinner

Friday 8 January 2010

• 9.30-9.45 Introduction to Break-out Sessions II (chaired by...):
  • Software & Data (Paul Thomas)
  • General facility access (?)
  • Access to specialised, pre-commercial equipment (?)
  • High-resolution microscopy (Rolly Wiegand)
  • Careers (Peter March)
• 9.45-11.00 Break-out sessions II
• 11.00-11.30 coffee
• 11.30-12.30 Summaries of break-out sessions + final discussions
• 12.30-13.30 lunch and option for FILM facility viewing

=> Doodle Poll: people's interests in topics

Date, time and location

The 'Doodle Poll - meeting dates' showed that many people can only do the first week of January, so the definitive date will now be Thursday 7 (lunch time) to Friday 8 January 2010 (lunch time).

The meeting will be held in the South Kensington campus of Imperial College London, 5th floor of the Sherfield Building / room SALC 5 (see Fac_Man_Meeting_2010_directions.pdf or GoogleMap for details). Walk into the campus from Exhibition Road, just around the corner from the Science Museum, and walk around the Queen's Lawn (with the big tower) in the middle of the campus.

This is ~30 min by public transport from Euston and Kings Cross railway stations, 10 min from Victoria station, or a 25 min walk across Hyde Park from Paddington (slightly longer on the Circle Line). For time tables and other stations, see Transport for London (TfL) Journey Planner.

Accomodation in walking distance from the meeting location can be booked at discounted rates (starting from £69) through the Imperial College Hotel Accomodation website. Many affordable hotels can also be found on South Kensington Hotels, many of them actually cheaper than through the Imperial College website and also in walking distance, but you need to check distance (e.g. TfL) and quality (e.g. Tripadvisor) yourself.

Travel and weather update

Update Thu 7 Jan 8:33:

Most trains across the country seem to run with only minor delays (under an hour), so the meeting will go ahead, maybe with a little extended lunch to give people more time to arrive. For travel updates see Transport for London, TravelDirect (train) and BAA (airport). The weather forecast for today and tomorrow is also pretty good (Metoffice and MetCheck).

Registration

Online registration is now closed, if you still want to attend please get in contact with m.spitaler@imperial.ac.uk

A list of participants is available on the registration page