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Instruments by Science Group

Macromolecular
Crystallography
Soft Condensed
Matter
Imaging and
Microscopy
Biological
Cryo-Imaging
Magnetic
Materials
Structures and
Surfaces
Crystallography
Spectroscopy

Contact

Admin enquiries

Tel: +44 (0) 1235 56 7480 
E-mail: EBICadmin@diamond.ac.uk

Science enquiries

Peijun Zhang
Tel: +44 (0) 1235 77 8878
E-mail: peijun.zhang@diamond.ac.uk

Daniel Clare
Tel: +44 (0) 1235 56 7501
E-mail: daniel.clare@diamond.ac.uk

Yuriy Chaban
Tel: +44 (0) 1235 77 8207
E-mail: yuriy.chaban@diamond.ac.uk

Karen Davies
Tel: +44 (0) 1235 77 8057
E-mail: karen.davies@diamond.ac.uk

Training enquiries

Kyle Morris
Tel: +44 (0) 1235 56 7537
E-mail: kyle.morris@diamond.ac.uk

Science Group Leader

Martin Walsh

Email: martin.walsh@diamond.ac.uk
Tel: +44 (0)1235 778518

Funded by a grant from

Wellcome Trust

MRC

BBSRC

eBIC

Status: Operational

Accelerating Voltages: 3-30, 200 & 300 kV

Cryo-EM: Cryo Electron Microscopy Cryo-ET: Cryo Electron Tomography Imaging Electron Microscope Electron Crystallography FIBSEM: Cryo Focused Ion Beam Scanning Electron Microscopy Microscopy
  1. Instruments
  2. Biological Cryo-Imaging
  3. eBIC
  4. User Guide

User Guide

Welcome to eBIC

Peijun Zhang <br/>eBIC Director
Peijun Zhang
eBIC Director


Congratulations on being awarded sessions using eBIC microscopes, our experienced team are looking forward to welcoming you to Diamond, and working with you at eBIC's state-of-the-art facility.

Please read carefully through the information provided on this page. These guidance notes give important advice, to help users prepare for microscope sessions with us.

Through experience we know that the better prepared our users are, the smoother their microscope sessions run, and this results in our users making best use of time using eBIC microscopes for their research.

Your forward planning and preparation is appreciated, this will help eBIC Local Contacts to best support you during your microscope session.

We look forward to working with you soon.

Grids & Samples Grids & Samples Sample Shipping Sample Shipping On-site Sessions On-site Sessions Remote Sessions Remote Sessions Guides & Info Guides & Info
  • Pre-session
  • BAG session
  • RAPID session
  • Post-session
  • Data and Processing

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 1 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 sample shipping.
     
  • 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.
     
  • Liaise with the Diamond User Office to make arrangements for visiting eBIC

BAG sessions

 

What guidance instructions are available for running a session?

  • Guides for user sessions are available: User guide instructions.


BAG proposal sessions:

  • BAG sessions may be longer than 48 hours
    eBIC recommends no more than 4 grids are loaded per 48hr session.
    The maximum number of grids which can be loaded at once is 11.
     
  • Samples loaded on first day of BAG session
    All samples will be loaded on the first day of a BAG session.
    A second load maybe possible for sessions which are longer than 4-days.

Schedule for a standard microscope session at eBIC:

  • Remote visits
    Users will be contacted by Local Contacts (LCs) prior to the start of a session,
    asking for data collection parameters. On the day of the session, users should check they can log on remotely after 9am and be ready to take over control of the microscope around 11am.
     
  • Onsite visits
    Local Contacts (LCs) will meet users at the i14 entrance and take them to the 
    control room. LCs will then load samples and set up the microscope with the aim that users can take control of the microscope at around 11am. 
     

Users are expected to provide samples suitable for continuous automated data collection and have enough samples to actively use the whole of the allocated time. 
 

The day's timetable will normally be:
09.00 Session starts.
09.00-10.30 Local Contact (LC) loads samples, tunes energy filter tuning and acquires gain reference.
10.30-11.30 Alignments and autofunctions checked.
11.00-12.00 LC hands over control to user.
11.30-12.30 Collect grid atlases.
12.30-14.00 Screen grids and choose which grid(s) to collect on.
14.00-16.00 Setup EPU/TOMO/SerialEM for automatic data collection.
16.00 Data collection should be in progress. Initiate on-the-fly processing.
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 plans to add more points after 5pm, please inform LC during working hours or send them an email to warn them that data collection will be interrupted.
 

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.

RAPID SESSIONS

 

What guidance instructions are available for running a session?

  • Guides for user sessions are available: User guide instructions.

RAPID proposal sessions:

  • Rapid proposals are usually 48 hours
    Successful Rapid proposals are allocated a 48hr slot during weekdays and
    either 48 or 72 hr slots at weekends starting on Fridays.
     
  • Successful Rapid proposals will be allocated time within six months of acceptance
    Rapid proposals are reviewed continuously.
    Successful proposals are allocated the next available rapid slot.
    Rapid proposals are only scheduled during Diamond run time (PDF) of which 10% is dedicated to Rapid sessions.


Schedule for a standard microscope session at eBIC:

  • Remote visits
    Users will be contacted by Local Contacts (LCs) prior to the start of a session,
    asking for data collection parameters. On the day of the session, users should check they can log on remotely after 9am and be ready to take over control of the microscope around 11am.
     
  • Onsite visits
    Local Contacts (LCs) will meet users at the i14 entrance and take them to the 
    control room. LCs will then load samples and set up the microscope with the aim that users can take control of the microscope at around 11am. 
     

Users are expected to provide samples suitable for continuous automated data collection and have enough samples to actively use the whole of the allocated time. 
 

The day's timetable will normally be:
09.00 Session starts.
09.00-10.30 Local Contact (LC) loads samples, tunes energy filter tuning and acquires gain reference.
10.30-11.30 Alignments and autofunctions checked.
11.00-12.00 LC hands over control to user.
11.30-12.30 Collect grid atlases.
12.30-14.00 Screen grids and choose which grid(s) to collect on.
14.00-16.00 Setup EPU/TOMO/SerialEM for automatic data collection.
16.00 Data collection should be in progress. Initiate on-the-fly processing.
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 plans to add more points after 5pm, please inform LC during working hours or send them an email to warn them that data collection will be interrupted.
 

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.


 

 

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