User Guide for Beamtime

Your application for beamtime (beamtime proposal) will be reviewed and evaluated by the proposal review panel 9 based on your science case. Please, refer to the section “Frequently asked questions” if you have more questions about proposal submission and deadlines. The section “Preparing a proposal in UAS” will help you to submit the proposal.

Beamline Staff will evaluate the technical feasibility of your beamtime application before the meeting of the proposal review panel. Beamline Staff do not make any decisions about the science case of your proposal and do not award the beamtime. The technical feasibility is reported to the proposal review panel who assess the science case. If your proposal is rated as technically not feasible, the beamtime will generally not be awarded. Beamline Staff can help you to evaluate the technical feasibility of your proposal before submission. Please, consider the huge demand on Beamline Staff for assistance before proposal submission deadlines and contact Beamline Staff not later than two weeks before deadline.

Before you submit your proposal, we would strongly recommend:

1) You should carefully read the information on the Beamline DIAD webpage. Contact Beamline Staff before proposal submission if you have any questions. It is mandatory for all proposals to have attended one of the weekly Zoom drop-in sessions to engage with one of DIAD’s scientists.

2) Simultaneous diffraction and tomography/radiography experiments are possible on the DIAD beamline, your experiment must utilise both imaging and diffraction. This a technical and scientific requirement.

3) Consider pathways to impact, is there a real world application for this experiment and is there a publication plan?

4) Beamline DIAD can provide some basic sample environments. The beamline can also accommodate users’ sample environments for in situ measurements. Please, check before proposal submission that it is technically feasible to bring your equipment.

5) Beamline DIAD is not identical to other beamlines at Diamond Light Source or to other diffraction or tomography beamlines at different synchrotron facilities. Please, consider the maximal X-ray flux on DIAD for both diffraction and imaging beams, when comparing it with other beamlines for fast diffraction or imaging measurements.

6) All samples and user equipment must comply with Diamond’s Safety Requirements. Please, ensure you carry out a proper risk assessment for the Experimental Risk Assessment section of your proposal.

When your proposal is accepted:

1) It is the responsibility of users to provide the detailed information about their sample environments and experimental procedures to Beamline Staff either in the proposal, or immediately after the beamtime is awarded.

2) Any equipment used to manipulate a sample before, during or after an experiment will be considered a sample environment. This includes tension rigs, heating/cooling stages/furnaces, pressure chamber etc. If you plan to bring a furnace or any other heating equipment: all heating equipment must be tested and heated to outgas prior to arrival at Diamond.

If you plan to bring equipment operating at high pressures: a current pressure test certificate is required. The certificate has to confirm that the equipment has been pressure-tested to 1.5 times of its operating pressure and has been tested within the last 2 years. The pressure equipment must not have been subsequently modified. Please, send the certificate to your Local Contact and to the Beamline Technician by the date stated in your notification email. You will not be permitted to operate your equipment without this document.

The use of uncontained, fibrous or friable materials such as Kaowool is forbidden. Loose fibres and dust from such materials can damage the beamline stage drive mechanisms and encoders. If in doubt, contact the Beamline Staff first.

Beryllium windows on any piece of user’s sample environment are not allowed on DIAD and must be replaced by alternative windows (glassy carbon, sapphire, etc.) before beamtime.

3) You can contact your Local Contact (or any member of the beamline if your experiment is not scheduled yet) about the pre-experimental visit to the beamline for considering the best way of installation and running your sample environment and your experiment.

Useful phone numbers and emails when planning the experiment or during your pre-experimental visit:

If you have any questions about accommodation, please contact the User Office. The User Office is open between 8:30 am and 4:30 pm from Monday to Friday.

When your experiment is scheduled:

1) Your experiment will be scheduled at the K11 experimental hutch. Please, check the description on the corresponding webpages and on the webpage Detectors.

2) Fill all necessary information in User Administration System (UAS) as soon as possible using the guidelines for users:

 - Please, book the accommodation for all members of your experimental team as soon as possible, as the number of available rooms in limited. All members of your experimental team must have a valid online safety instruction before you can book the accommodation. If necessary, members of your experimental team must apply for business visa as soon as possible to get it in time for your beamtime; contact User Office for invitation letter.

 - Your Experimental Risk Assessment in User Administration System must be submitted well in advance of your beamtime (no later than 15 working days), so Diamond Health and Safety team will be able to evaluate it in time for your experiment.

- Principal Investigator of the proposal must ensure that all members of their experimental team are competent to perform the experiment and operate the sample environment.

3) If you plan to perform the diffraction experiment, all members of your experimental team should be familiar with program DAWN.

4) Prepare your portable hard drives for saving a copy of your data. Only hard drives without password protection, formatted under Linux or Windows (excluding exFat) can be used. The usual size of diffraction data collected during 3 days at I12 can be 500 GB; the size of tomography data collected during 3 days at I12 can be several TB or more. Due to the large size of tomography datasets, particularly from time resolved experiments, we recommend remote data transfer to your university via Globus.

We strongly recommend you set up your portable hard drives on the data dispenser in Data Analysis room before measurements. In this case all collected data will be automatically saved to your drives.

Normal working hours of the Beamline Staff (including your Local Contact) is 9 am – 5 pm during Mon – Fri. During normal working hours, your Local Contact or another member of the beamline team should be able to help you. Out of hours, please contact the Experiment Hall Coordinators (EHCs).

1) Remove your equipment from Experimental Hutch and laboratory and make them tidy. Clean your preparation area.

2) Remove all your samples. Please, do not leave any your samples in Experimental Hutch, beamline laboratories, in the refrigerator or in the drying oven, or in any additional laboratories.

3) Un-mount your hard drive.

4) You are expected to submit experimental report within six months after beamtime (it will be taken into account by proposal review panel if you submit another beamtime application later).

5) If you need to retrieve your data remotely, use the corresponding IT guidelines.

6) The number of proposal and the acknowledgement to Diamond Light Source should be presented in the section Acknowledgement of your publications with results obtained at beamline I12. Please, follow the official Diamond Guidelines for Publications.

7) All Diamond users are required to inform Diamond of publications resulting from their research according to official Diamond Guidelines.

The reference for the Beamline DIAD publication (should be used in all publications which include results measured on DIAD):

• In publication

If you used the program DAWN for powder diffraction calibration and data reduction, the corresponding references are:

1) M. Basham, J. Filik, M. T. Wharmby, P. C. Y. Chang, B. El Kassaby, M. Gerring, J. Aishima, K. Levik, B. C. A. Pulford, I. Sikharulidze, D. Sneddon, M. Webber, S. S. Dhesi, F. Maccherozzi, O. Svensson, S. Brockhauser, G. Naray, A. W. Ashton. “Data Analysis WorkbeNch (DAWN)”. J. Synchrotron Rad. (2015). 22, 853–858. (link)

2) J. Filik, A. W. Ashton, P. C. Y. Chang, P. A. Chater, S. J. Day, M. Drakopoulos, M. W. Gerring, M. L. Hart, O. V. Magdysyuk, S. Michalik, A. Smith, C. C. Tang, N. J. Terrill, M. T. Wharmby, H. Wilhelm. “Processing two-dimensional X-ray diffraction and small-angle scattering data in DAWN 2”. J. Appl. Cryst. (2017). 50, 959–966. (link)

3) M. L. Hart, M. Drakopoulos, C. Reinhard, T. Connolley. “Complete elliptical ring geometry provides energy and instrument calibration for synchrotron-based two-dimensional X-ray diffraction”. J. Appl. Cryst. (2013). 46, 1249–1260. (link)

If you used the program Savu for reconstruction of tomography data or for correction of radiography data, the corresponding references are:

1) N. Wadeson and M. Basham, “Savu: a Python-based, MPI framework for simultaneous processing of multiple, N-dimensional, large tomography datasets”. (2016). arXiv:1610.08015 (link)

When you used tomography reconstruction plugins in Savu, the corresponding additional references are:

- for Paganin plugin (contrast enhancement, plugin PaganinFilter):

2) D. Paganin, S. C. Mayo, T. E. Gureyev, P. R. Miller, S. W. Wilkins. "Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object". Journal of Microscopy, (2002). 206(1), 33-40. (link)

- for zinger removal plugin (Desinger or DesingerGpu):

2) R.C. Atwood, A.J. Bodey, S.W.T. Price, M. Basham, and M. Drakopoulos. "A high-throughput system for high-quality tomographic reconstruction of large datasets at diamond Light Source". Philos. Trans. A. Math. Phys. Eng. Sci., (2015). 373, 20140398. (link)

- for lens distortion correction plugin (DistortionCorrection):

2) N.T. Vo, R.C. Atwood, M. Drakopoulos. "Radial lens distortion correction with sub-pixel accuracy for X-ray micro-tomography". Opt. Express, (2015). 23, 32859-32868. (link)

- for automatic determination of the centre of rotation (VoCentering; not applicable for manual determination of the centre of rotation and for double field of view tomography):

2) N.T. Vo, M. Drakopoulos, R.C. Atwood, C. Reinhard. "Reliable method for calculating the center of rotation in parallel-beam tomography", Opt. Express, (2014). 22, 19078-19086. (link)

- for ring artifacts removal (plugins PemoveAllrings, RemoveLargeRings, RemoveUnresponsiveAndFluctuatingRings, RingRemovalFiltering, RingRemovalFitting, RingRemovalInterpolation, RingRemovalSorting):

2) N.T. Vo, R.C. Atwood, M. Drakopoulos. "Superior techniques for eliminating ring artifacts in X-ray micro-tomography", Opt. Express, (2018). 26, 28396-28412. (link)

- for CCPI ring artifacts removal (plugin CcpiRingArtefactFilter)

2) S. Titarenko, P.J. Withers, A. Yagola. "An analytical formula for ring artefact suppression in X-ray tomography", Appl. Math. Lett., (2010). 23(12), 1489–1495. (link)

- for wavelet-fft method (plugin RingRemovalWaveletfft):

2) B. Münch, P. Trtik, F. Marone, M. Stampanoni, "Stripe and ring artifact removal with combined wavelet — Fourier filtering", Opt. Express, (2009). 17, 8567-8591. (link)

- for Raven’s method (plugin RavenFilter):

2) C. Raven, "Numerical Removal of Ring Artifacts in Microtomography", Rev. Sci. Instrum., (1998). 69(8), 2978–2980. (link)

- for regularization-based CCPI denoising method (plugin CcpiDenoisingGpu or CcpiDenoisingGpu3d):

2) V. Titarenko, R. Bradley, C. Martin, P.J. Withers, S. Titarenko. "Regularization methods for inverse problems in x-ray tomography", Proc. SPIE 7804, Developments in X-Ray Tomography VII, 78040Z (1 September 2010). (link)

- for Astra toolbox:

3) W. van Aarle, W. J. Palenstijn, J. Cant, E. Janssens, F. Bleichrodt, A. Dabravolski, J. De Beenhouwer, K. J. Batenburg, and J. Sijbers, “Fast and Flexible X-ray Tomography Using the ASTRA Toolbox”. Optics Express, (2016). 24(22), 25129-25147. (link)

4) if FBP in Astra toolbox was used: G. N. Ramachandran, A. V. Lakshminarayanan, “Three dimensional reconstructions from radiographs and electron micrographs: Application of convolution instead of Fourier transforms”. Proc. Nat. Acad. Sci., (1971). 68, 2236-2240. (link)

if SIRT in Astra toolbox was used: P. Gilbert, “Iterative methods for the reconstruction of three-dimensional objects from their projections”. J. Theor. Biol., (1972). 36, 105-117. (link)

if SART in Astra toolbox was used: A. H. Andersen, A. C. Kak “Simultaneous algebraic reconstruction technique (SART): A superior implementation of the art algorithm”. Ultrason. Imaging, (1984). 6, 81-94. (link)

if CGLS in Astra toolbox was used: M. R. Hestenes, E. Stiefel. “Methods of conjugate gradients for solving linear systems”. Journal of Research of the National Bureau of Standards, (1952). 49(6), 409-436. (link)

- for Tomopy:

3) D. Gürsoy, F. De Carlo, X, Xiao, C Jacobsen. "Tomopy: a framework for the analysis of synchrotron tomographic data". J. Synchrotron Rad., (2014). 21(5), 1188–1193. (link)

4) if gridrec (i.e direct Fourier inversion method) in Tomopy was used: J.D. O'Sullivan. "A fast sinc function gridding algorithm for Fourier inversion in computer tomography". IEEE T Med. Imaging. (1985). 4, 200–207. (link)

Post-experiment Data Analysis visits are possible for users to evaluate their data. These visits aim to support independent work by users, most frequently to make use of commercial Avizo program for tomography data visualisation and analysis. Beamline staff has no resources to train users in Avizo. Users are advised to join the training course elsewhere before the data analysis visit.

You must contact your Local Contact at least 2 weeks before the planned Data Analysis visit to ensure the availability of the corresponding workstations (i.e. that no other users were already booked) and to retrieve your data from archive if necessary.