Quick reference guides
Before an eBIC session
What are facilities like at eBIC?
eBIC is housed in a modern, purpose built facility, with microscopes located on the ground floor, with the exception of Titan Krios I which is a short walk away in Diamond's synchrotron building.
Samples are clipped in the laboratory space on the ground floor and loaded onto microscopes, then data collection is managed remotely from the Control Room (located on the 1st floor of the i14 building).
eBIC users who visit site have use of break-out areas and a kitchen (with tea/coffee & drinking water, plus the use of a fridge & microwave). A short stroll across the road is the on-site restaurant, where meals & snacks can be purchased.
Accommodation for eBIC visitors is normally booked at the on-site guest house, which is within easy walking distance of the eBIC facility. The Diamond User Office organise accommodation bookings for rooms, with breakfast included.
What needs to be organised ahead of microscope sessions?
- Good quality samples required for the first day of a session
Follow this link for further details on grids and samples.
- Register samples and ship dewar to eBIC using Diamond systems
Follow this link for details on shipping samples.
- Liaise with the Diamond User Office to make arrangements for visiting eBIC
- eBIC recommend users consider the imaging conditions and detector they wish to use, prior to visiting. Users are welcome to contact eBIC staff with specific questions prior to the visit.
During an eBIC session
What guidance instructions are available for running a session?
- Guides for user sessions are available: User guide instructions.
- Please also refer to eBIC's video guides page (TBA).
BAG proposal sessions:
- BAG sessions may be longer than 48 hours
However, eBIC recommend that each sample is given a 48 hour slot.
- Samples loaded on first day of BAG session
Preferably all samples will be loaded on the first day of the BAG session, but new samples can be loaded every 48 hours.
RAPID proposal sessions:
- Normally 48 hour time slots allocated for Rapid proposals
Successful Rapid proposals will be scheduled microscope time, which will often be allocated in 48 hour slots.
- Sometimes Rapid proposal Friday sessions are 72 hours
For sessions scheduled on a Friday, 72 hours may be given depending on microscope cryo-cycles.
Schedule for a standard microscope session at eBIC:
Users meet their eBIC local contact either remotely or at the entrance hall of the i14/eBIC building on the first day of their session.
Users will be expected to be available during office hours on the first day either in person or via a telephone or video call, and provide suitable samples for automated data collection to run for the following 40 hours.
|The day's timetable will normally be:|
|09.15-10.15||Load up to 4 grids into Auto Grid cartridges & Krios cassette.|
|10.20-10.30||Load Auto Grid cassette into the Krios.|
|10.30-11.00||Local Contact performs alignments and camera calibrations.|
|11.00-12.00||Control given to user - Survey grids to determine the best grid.|
|12.00-12.45||Collect grid atlas image.|
|12.45-15.00||Setup EPU/TOMO/SerialEM, microscope alignments, detector gain references.|
|15.00-16.00||Check images, assess CTF and particle density.|
|16.00 onwards||Automatic data collection for ~40 hours.
The responsibility for monitoring an ongoing data collection resides with the user and instructions on how to do this can be found here.
If a user observes an issue with ongoing data collection the user needs to inform the EHCs on 01235 778787, who will communicate the issue to a Local Contact as required.
After an eBIC session
What needs to be organised after microscope sessions?
- Return dewars to home institute
eBIC users complete a Diamond dewar dispatch form. Dewars can be sent using Diamond's shipping agents. Diamond pay for sample shipping for UK users using Diamond shipping agents, 2 dewars per shift. Follow this link for details about returning a dewar.
- Experimental report
Diamond require users to promptly submit an experimental report through the User Administration System UAS upon returning to the home establishment.
- Publishing work
Users publishing work containing data from eBIC should ensure they:
|Acknowledge Diamond Light Source and any of its personnel in any published material that results from use of the cryo-EM facilities.|
|The following statement should always be included in any publications: "(We acknowledge) Diamond for access and support of the cryo-EM facilities at the UK national electron Bio-Imaging Centre (eBIC), proposal EM####, funded by the Wellcome Trust, MRC and BBSRC."|
|Notify Diamond of the title, authors, facility, journal and reference number, date of acceptance and publication of any scientific publications or papers as a result of a user's use of eBIC microscopes.|
|Notify Diamond if a user plans to publish any materials e.g. general reports, press releases, etc. that result from their use of eBIC microscopes, prior to the material being published. Allow time for Diamond to review such material and give its prior permission to publish such material if reasonably requested by Diamond.|
Data and processing at eBIC
How is data stored?
- Raw data - archived
All raw data are permanently archived by Diamond to tape media but remain accessible on spinning disk for 40 days.
- HDD backup - no longer supported
Support for HDD backups has been phased out and users should copy their data via high bandwidth file tansfer systems such as Globus or SFTP. Follow this link for the Remote access and analysis: User guide.
- Data backup - eBIC users responsible
eBIC users are responsible for backing up data, to transfer it to local systems and provide long term data storage: Diamond data back up.
Monitoring an ongoing data collection
- eBIC users responsible
The responsibility for monitoring an ongoing data collection session resides with the user.
- How to monitor?
Instructions on how to monitor an ongoing data collection can be found in the Remote access and analysis: User guide.
- Contact EHC with any issues
If a user observes an issue with ongoing data collection, eBIC request that the user informs the Experimental Hall Coordinators (EHC) on +44 (0) 1235 778787. The EHC will communicate the issue to a Local Contact as required.
|Collaborative Computational Project for electron cryo-microscopy (CCP-EM)|
|The CCP-EM exists to support users and developers in the biological electron microscopy community.|
|Located in the Research Complex at Harwell (RCaH), adjacent to Diamond.|
|The core STFC team of CCP-EM are on hand to provide support and expertise to eBIC users, supplying them with access to the most advanced biological electron microscopy software available.|