Imaging and Medical
IMBL IS OFFERING THE FOLLOWING 3 OPERATING MODES:
- 2-Dimensional imaging of live animals, and 3-Dimensional imaging of materials in hutch 3B
- Fast computed tomography (CT) of small objects in hutch 2B
- Micro-beam radiation therapy (MRT) in hutches 1B and hutch 2B
PREPARING FOR BEAMTIME APPLICATIONS
For information on how to prepare your application and more detail on the available options refer to the Beamtime on this beamline (IMBL) information page.
For experiments using live animals first read the guidance provided.
Animal ethics procedures must be addressed well in advance of submission of the beamtime proposal.
• For transmission FTIR microanalysis of thin samples we strongly recommend that your samples are mounted on IR transmitting windows such as CaF2 (cut-off 50 %T at 900 cm-1 for 0.5 mm thick window), BaF2 (cut-off 50 %T at 750 cm-1 for 0.5 mm thick window), or ZnSe (cut-off 50 %T at 500 cm-1 for 0.5 mm thick window). We do not recommend the use of IR reflective slides, such as Kevley slides, for “transflectance” measurements.
• A limited supply of windows of various dimensions is kept at the beamline, but we recommend purchasing your own windows to enable you to prepare your samples prior to your beamtime. Further information on the material properties, and availability, of a wide range of window materials is available on the website of Crystran Ltd.:
• For thin sectioning of samples, a microtome is available on-site for use during your beamtime. HOWEVER we strongly recommend that any sectioning required is performed before your beamtime to save time while you are at the beamline. Please contact the beamline staff for advice on sample thickness and sample preparation.
• A microcompression cell is available with diamond windows for flattening of sample sections, or crushing of harder materials.
Micro ATR measurements
• A micro ATR objective is available for use and can be used for ATR mapping of sample surfaces and embedded materials. Two germanium crystal sizes (100 µm and 250 µm diameter) are available for hard and less hard materials respectively. The sample surface must be polished or microtomed flat (to approximately 1-5 µm roughness, depending on hardness) to ensure good optical contact between the ATR crystal and your sample. Please indicate in your proposal if this is required.
• For ATR spectroscopy of soft samples (e.g. biological materials or lipid coatings) please contact the beamline staff to discuss your requirements as the conventional micro ATR objective will probably produce too much force for analysis of our materials.
Grazing angle studies of surfaces
• A Grazing Angle Objective (GAO) is currently available and is suitable for the study of thin coatings on reflective metallic surfaces. Contact beamline staff for more details if this is required. Lateral resolution with the GAO is approximately 20 µm.
Sample heating stage
• A Linkam heated sample stage is available for use. This can cool samples to close to liquid nitrogen temperature and heat to 600 °C. As a longer working distance is required to accommodate the Linkam stage, the 15x objective used with this device will give a reduced lateral resolution of approximately 10 µm Contact beamline staff for more details if this is required.
Live biological samples
• Sample chambers dedicated to the study of live cells in a liquid environment have been developed by the IR beamline staff, and are under continued development. These are suitable for both static (approximate hold time of 30 minutes) and continuous flow conditions. The use of CaF2 windows in our liquid cells currently limits the spectral range available to approximately 1000 cm-1.
• Class II containment facilities are available within the Biochemistry support laboratory for the preparation of cell cultures. Users requiring access to this facility should contact IR beamline staff prior to submitting a proposal.
Off-line Focal Plane Array IR microscope
• The off-line Focal Plane Array FTIR microscope is currently available for booking in conjunction with your beamtime proposals, if successful. Contact beamline staff if this is required.
For more details of the instrumentation available at the IRM beamline, please see the web page below, or contact the beamline staff:
Beamline Contact: email@example.com
THz / Far-IR
The following instruments are available to users from May 2015:
- An Enclosive Flow Cooling (EFC) cell with multipass optics is available for the study of gases & molecular clusters at cryogenic temperatures. The EFC cell is generally operated at temperatures ranging from79-300 K, but can also be operated with liquid helium. The cell can be equipped with TPX, PE, or KBr windows offering spectral coverage from 10-4000 cm-1; with a base optical path length of 0.65 m, it can achieve path lengths up to 27 m.
- 2 room temperature multipass glass gas-cells: one of them can be coupled to furnace for the study of short-lived molecules, and can offer a path length up to 20 m, while the other designated for non-reactive gases can offer up to 30 m in path length.
- A 10 cm single pass gas-cell designed to mix gases in-situ
- A Janis ST-100 cryostat to study solid homogeneous samples in transmission down to 77 K.
- A Cryo Industries of America closed-loop pulse tube (CLPT) cryostat to study solid homogeneous samples in transmission down to 6.3 K.
- A Grazing Incidence Angle (30-80 ̊) (GIA) accessory that is ideal for the study of thin samples or surfaces at grazing angles at room temperature
- A Near-Normal Incident (11̊) Transmission/Reflection Optics (N2ITRO) accessory ideal for the study of optical properties of materials; it can be equipped with a far-ir polarizer.
The following instruments are offered to expert users only:
- A room-temperature 15 cm multipass gas-cell coupled to a 25W CO2 laser operating at 10.6 μm, or a 4.8 W Ar ion laser operating at 1064 nm, 532 nm, 355, nm and 266 nm to generate short-lived molecules by photolysis, and can offer path lengths up to 3 m.
- A furnace to generate short-lived species by pyrolysis that can be coupled to the EFC cell
- A Linkam based furnace for the study of solids up to 1000 K; it can also be coupled to the N2ITRO setup.
- A vacuum-proof cell for qualitative and quantitative analysis of liquid samples; the cell is equipped with polyethylene, and spacers ranging from 6-250 microns.
- A Grazing Incidence Angle optical setup combined with the ST-100 cryostat for the study of thin samples or surfaces at grazing angle at low-temperatures
- Diamond Anvil Cell
- Laser excitation using a 25W CO2 laser operating at 10.6 µm, or a 4.8 W Ar ion laser operating at 1064 nm, 532 nm and 266 nm to generate short-lived molecules or to induce chemical changes by photolysis
Please contact the THz/Far-IR beamline staff if you wish to use any of these instruments or if you would like to discuss a potential experiment.
Beamline Contact: firstname.lastname@example.org
MX1: MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINE
- Energy range from 5.5 - 18 keV
- User changeable energy from 8.5 to 17.5 keV
- Fluorescence scans for MAD and metal identification
- UV laser for radiation damage induced phasing
- Robotic loading and remote access
- Rapid access is available
MX2: MICRO CRYSTALLOGRAPHY BEAMLINE
- Energy range from 4.8 - 20.0 keV
- User changeable energy from 8.5 to 15.5 keV
- Microfocus beam with FWHM of 25x15 microns (HxV)
- Beamline operating modes: channel cut (fixed energy at 13 keV) and double crystal
- High flux with up to 3e12 ph/s/mm2 in the focussed beam
- Fluorescence scans for MAD and metal identification
- User-changeable micro-collimator with 20, 10, and 7.5 micron apertures
- Robotic loading and remote access
- Rapid access is available
More info on technical updates page.
Beamline Contact: email@example.com
- Users can find tips on proposal preparation under Beamtime on this beamline on the powder diffraction beamlines' webpage.
- Proposers interested in performing total scattering experiments should consult the Total Scattering Analysis page and prepare their proposal accordingly.
- All proposals must be accompanied by evidence of previous diffraction measurements; i.e. a laboratory or synchrotron powder diffraction pattern that is indicative of the data obtained from the sample(s) of interest.
- Experiments at high pressure are complex and users new to the technique should contact beamline staff before submitting their proposals
The detectors which are currently available are:
- Mythen microstrip
- Photonic Sciences VHR CCD
- MAR165 CCD
- Details of the ancillaries available at the beamline can be found under Sample stages and Environments.
- Users should, as much as possible, select all of the appropriate ancillaries for their proposed experiment using the list of options within the portal
- Note that users seeking to use their own sample stage and/or ancillaries should discuss this in advance with the powder diffraction beamline staff AND provide drawings of the equipment to show how it is anticipated that this equipment will fit at the end station
- Available for experiments are:
- Cryostream (80 - 450 K)
- Hot-air blower (100 - 900 °C)
- Anton Paar strip furnace (25 - 2300 °C)
- STOE capillary furnace (25 - 1100 °C)
- Gas/vacuum flow cell for capillary samples
- High-throughput stage
- Cryostat for samples in transmission geometry (10 - 300 K)
- Diamond Anvil Cell (DAC) at ambient temperature only
The typical consumables required for most experiments on the Powder Difrraction beamline are listed below. A significant reduction in the beamline consumables budget has necessitated a number of new policies to come into effect that will affect those experiments requiring the use of the Anton Paar furnace and the DAC specifically.
- Quartz and borosilicate capillaries can be purchased from hilgenberg remember to allow plenty of time to order your capillaries as the beamline does not provide them.
- For experiments requiring pressures: 5 - 10 bar, quartz capillaries with a wall thickness of 0.02 mm are required.
- For experiments requiring pressures: 10 – 20 bar, quartz capillaries with a wall thickness of 0.05 mm are required.
- Sapphire capillaries are required for experiments using the capillary furnace for temperatures >1100°C and those experiments requiring pressures greater than 2 MPa (20 bar).
- For experiments using the Norby or capillary flow cell, graphite Supelco M2-A ferrules are also required and can be obtained from here.
Anton Paar furnace experiments
- Anton Paar furnace experiments requiring either platinum or tungsten heating strips must be supplied by Users.
- The heating strips can be purchased from Anton Paar, see here for more details.
- For experiments requiring temperatures 900°C or less, inconel heating strips may be used and are available for Users.
High pressure Diamond Anvil Cell (DAC) experiments
For experiments at pressures >10 GPa users will need to provide their own diamonds and seats. They can be purchased from: https://www.diamondanvils.com/ or http://www.almax-industries.com/ . Users must consult beamline staff for more information before purchasing.
HIGH PRESSURE AND TEMPERATURE CONDITIONS AVAILABLE AT THE POWDER DIFFRACTION BEAMLINE
Capillary Flow Cell Experiments
The maximum pressure at the beamline in a capillary is 2 MPa (thick-walled capillaries required as above) unless prior agreement is reached with beamline staff.
For experiments which use > 5% Hydrogen gas, the maximum temperature which can be used is 500°C.
Capillary Furnace Experiments
The maximum operating temperature is 1100°C for quartz capillaries
The maximum operating temperature is 1350°C for sapphire capillaries.
Beamline Contact: firstname.lastname@example.org
Soft X-ray Spectroscopy
- The beamline continues to operate well, and recent tests with the undulator mean we can now offer the potential of rotating the linear polarisation of the x-ray beam. For small samples this offers an easier method of making a polarisation analysis than by rotating the sample.
- The beamline has new thermal evaporation sources. One source is optimised for organic evaporants in the temperature range from 50 to 300°C. The other is optimised for 200-800°C, but can operate to 1100°C with a suitable crucible. The beamline would prefer to offer these systems to users who wish to thermally evaporate material. A higher temperature evaporator, to 1400°C, may also be available. Further information on source specifications can be found in the beamline technical pages. We have a supply of crucibles available which we will exchange for each new evaporant. We are happy to support users who wish to use the full in situ surface science capabilities of the beamline. We are also happy to discuss how we can extend our capabilities, but we cannot guarantee that we will be able to do this in every case.
- A new 4 point probe for measuring the surface conductivity of samples in UHV has been installed and tested in the preparation chamber. This is a specialist device that can be useful for a limited range of experiments. As an experimenter you will probably have knowledge of the information that can be obtained using such a device. If this would be useful as an adjunct to your experiment please contact us to discuss its use during your experiment. We are not offering this device as a general part of the user environment.
- The beamline scientists of the soft x-ray beamline are very happy to hear directly from potential users and we would urge you if you would like to perform an experiment on this beamline to email or telephone us directly. For information, the beamline contact address below sends your email to all three beamline scientists.
Beamline Contact: email@example.com
Small and Wide Angle X-ray Scattering
One to Two Shift Access for Protein Solution Scattering
The SAXS/WAXS beamline is now able to support a limited number per cycle of 1 or 2 shift experiments for protein solution scattering. This option is aimed at:
- encouraging, facilitating and training new Users of SAXS who don’t need a full 24 hours of beamtime, but have a strong case for synchrotron solution SAXS time. For new protein Users experiments, you can now apply for a one shift experiment which would be run during the day and have close staffing support to help train you to run the beamline and help start you on basic data processing and analysis.
- experienced groups who need 1-2 shifts of beamtime to complete a previous experiment, particularly if anticipated to complete a publication or a piece of research. In such cases, experiments would most likely commence at 4pm and run overnight, hence previous experience running the beamline is essential.
Please note there are some key technical and operational constraints needed to make short access experiments feasible:
- Short access (less than 24 hours) is only available for solution scattering experiments given its well established and fixed experimental setup. The wide variety and custom requirements of many materials science measurements is not suited to allocations under 24 hours.
- Only a 2.68 m camera length at 12 keV will be available, and no camera length changes would be allowed. This covers 0.006 to 0.35 Å-1and suits the majority of proteins from ~ 10 to 300 kDa (smaller for highly extended proteins). This standard setup would normally be ready to use at the start of beamtime with a minimum of setup and delay.
- Both autoloaded static samples (50 – 100 microlitres), and size exclusion chromatography will be available. If you are using SEC, we recommend you pre-equilibrate your column(s).
- For experiments commencing at 4pm, the Experiment Spokesperson must be an experienced User of the beamline, able to run the beamline and lead their experiment group without training from the beamline staff. We need to know who your spokesperson is likely to be in the proposal, and will require this information in the Detailed Experiment form in order to approve the experiment.
- The number of people provided travel support by AS may be less than 3.
- Short access experiments would be submitted, reviewed and scheduled at the same time and through the same process all other proposals. This is not a rapid access scheme.
- For evening starts, consider arriving early to potentially equilibrate columns on site, and/or prepare and configure plates ready for analysis.
Guidance for Proposals
Short access proposal go through the same submission and review system as all other proposals, and uses exactly the same online form as all other proposals (i.e. there is no special form for short-access proposals), experiments.:
- Just indicate the number of shifts (of 8 hours each) you estimate you need. If this is less than 3 shifts, this automatically identifies it to the review process as a short request.
- In the proposal (for example in the track record section) describe whether you are new to SAXS and therefore need to be scheduled from 8 am. If you are an experienced User and able to make use of 4pm -8 am scheduling, you will need to declare who will be the likely on-site experiment spokesperson to lead the experiment.
The short access scheme for proteins is not a substitute for laboratory SAXS. As for all protein experiment proposals, make sure you explain why synchrotron SAXS is needed rather than a laboratory SAXS instrument. We strongly advise you provide evidence that samples have been adequately screened/characterised as suitable for synchrotron SAXS (e.g. include basic data in the Figures section such as gels, SEC traces, light scattering, AUC etc.).
The number of short experiments allocated in a cycle will depend on the ranking of review scores, and the capacity of the beamline to sustainably support more experiments amongst already busy operations. We envisage trialling this access pathway on a small scale to assess the impact on scientific output (i.e. will this prove a productive mode of access), its impact on staffing, and the potential impact on experienced Users running 2-shift experiments starting in the evening.
Minibeam: A New Capability
Until recently the beamline has had a very limited ability to produce a beam at the sample position significantly smaller than its focal size (which is currently ~250 x 120 micron H/V FWHM). This has been a fundamental aspect of the optical design of the beamline which is designed to convert the storage ring properties for low-q SAXS (0.001Å-1 at 8 keV), which generally mandates a moderate beamsize. The main slit layout has been optimised for low-q performance, so normally the beamsize defined by the focal properties of the beamline.
In April 2015, an additional slit was installed on the beamline not far from the focal point. The original low-q capability of the beamline is still available and will remain the standard setup for general SAXS use. However, the new slits add the option to produce small beams well below the focal size still to quite low q (with some constraints about camera length and photon energy described below). The final guard slit is able to control slit scattering to produce good q-minimum ranges, albeit with limitations due to the much shorter collimation length than the standard setup. Because this is done with slits rather than additional or upgraded focussing, which is considerably more expensive and an intended longer term upgrade, there is significantly less flux than the full beam. However, it may still be adequate flux for your needs, especially if you are not particularly limited by exposure time. These new slits allow better definition of small beams when required, with much more flux than was previously possible.
Percentage of full flux vs approximate full width size (µm) for minibeam setup. Area shaded darker grey with bold text are maximum limits for 7m camera and can only be used at 12-18 keV. Area shaded lighter grey with underlined text can are maximum limits for 3.3 m camera and can be used at any energy. Larger settings (white, plain text) can be used at 1.5 m or shorter camera lengths at any energy. Settings smaller than maximum for each camera length can always be used. Please note exact beam sizes below 50 µm are quite approximate and have not yet been measured in detail. Also, please note these numbers are currently full width sizes rather than full-width at half maximum because more characterisation of minibeam is still required.
Applications of minbeam mode
The most obvious applications of small beam modes are:
- Analysis or rastering of heterogeneous samples at higher spatial resolutions (e.g. 50 micron spatial resolution)
- Small samples, such as fibres. By limiting the beam size in one direction (e.g. vertical) to size of fibre you can increase signal:noise.
- Grazing incidence, to help control the footprint of the beam within the length of the specimen
- Smaller capillaries and microfluidics. Not only can the size of the bright part of the beam be constrained, so can the width of the background intensity that affects the minimum working diameter of capillaries. It should be straightforward to use 0.5 mm capillaries where desired (however this reduces sample scattering power and sample:glass thickness ratio).
Beamline Contact: firstname.lastname@example.org
X-ray Absorption Spectroscopy
- The available energy range is 5 - 31 keV via the following operational modes:
Mode 1*: 5 - 9 keV using Si(111)
Mode 2: 8.5 - 18.5 keV using Si(111)
Mode 3: 15 - 31 keV using Si(311)
*Note that in Hutch C the lowest accessible energy is 7 keV (Fe K edge)
- A proposal guidelines document has been prepared by the Proposal Advisory Committee (PAC) and the beamline team. Please read these guideliens carefully and follow them diligently as they give important information on how to write a sound proposal for access to the XAS beamline. Failure to follow the guidelines makes it difficult for the PAC and beamline scientists to assess the viability of an experiment, thus likely rendering a proposal less competitive.
- Proposals will necessarily be grouped together based on their energy range / operational mode and each proposal will only be allocated time for a SINGLE mode. If you need access to more than one beamline mode, please submit TWO separate proposals, one for each mode, and indicate that they are linked.
- For fluorescence measurements an estimate of the absorber concentration is needed to assess feasibility. Typical scan times are 20 minutes for XANES and 45 minutes for EXAFS.
- Standard experiments, that is where samples are mounted using standard sample holders and analysed at room temperature or in the He cryostat at 10K, are available in the first experimental station (Hutch B). Hutch B has 3 ion chambers and a 100 element Ge fluorescence detector. The setup in this end station is fixed and cannot be modified.
- Non-standard experiments are run in the second experimental station (Hutch C). Hutch C is currently available for transmission type experiments, e.g. for in-situ heater work. You need to contact the beamline team BEFORE you submit a proposal that seeks access to Hutch C. Please note that the lowest accessible energy in Hutch C is the Fe K-edge at 7 keV.
- Fast shutter, soller slits, and filters are available in Hutch B for fluorescence experiments.
- A sample cryostat is available for use in Hutch B. Although the cryostat is vibration-less, as a matter of good XAS practice, samples always need to be prepared as homogeneously as possible in order to promote good spectral results.
- The fluorescence detector readout time (overhead) is about 1 s per point.
- We also have a PIPS fluorescence detector, which can be useful for certain experiments. This type of detector is not energy resolving and can be used for non-complex samples where the concentration of the element of interest is around a few 1000s ppm.
- We need you to contact us before you submit any non-standard (Hutch C) experiment proposal, or if you have not used the XAS beamline before. Please contact us via email@example.com
X-ray Fluorescence Microscopy
Incident energy range: 4.2 to ~22 keV
Incident energy resolution: DeltaE/E = 10-4
KB mirror microprobe: ~1 μm focal spot. Stage range 100 mm * 100 mm. Can be used with Vortex or Maia detector
Cryostream in commissioning 2014r3, should be ready for use in 2015. Contact Martin de Jonge to discuss if interested.
Fast stages and tomography in commissioning also; should be available in 2015. Contact Martin de Jonge to discuss
Zone plate nanoprobe achieves focal spot down to 80 nm (8 keV). Energy range 7 keV - 11 keV typical. Sensitivity and spot size (resolution) can be traded off against one-another - resolution is 200 nm for typical geological concentrations, 300 nm for typical environmental concentrations, and 500 nm for biological concentrations. Can be used with Vortex detector (by default) or Maia detector (by special arrangement and subject to availability).
Recent studies in sources of elemental background and spectral noise have improved sensitivity to (eg) Zn by a factor of 5; however, sub-Ar metals are still poorly imaged due to the absence of a He atmosphere. This will be investigated in the next developmental step, due by ~mid 2015.
'Milliprobe' / large area scanner is under commissioning 2014r3 / 2015r1. Beam is defined by the exit silt, and so typical resolution is 200-μm. Capable of scanning objects of order 600-mm by 1200-mm, principally artworks. With some effort (and call for need) could be used for mapping western-blots simultaneously with the use of the microprobes. Contact Daryl Howard to discuss if interested.
Vortex: silicon drift diode detector. Detector orientation: 90-degree. Energy sensitivity above 1.6 keV; energy resolution ~140 eV. Typical dwell 0.2-2 sec/pixel. Can be used with either the ZP Nanoprobe or the KB microprobe.
Maia: 384-element silicon array detector for on-the-fly acquisition in 180 degree ‘backscatter’ geometry. Energy sensitivity 3.3 to 19.5 keV; energy resolution 300-400 eV. Typical dwell 0.5-50 msec/pixel. Default operation is on KB mirror microprobe; ZP nanoprobe by arrangement and subject to availability. While this detector is extremely reliable, it is a research detector and so we do not carry a complete spare. As such, it is available on a best-effort basis: every experiment should anticipate using the Vortex detector as a back up if required.
UPDATE: Maia Rev B should be available by early 2015. Rev B has improved low energy sensitivity, and so should be able to map S (~2.2 keV), and possibly P (~2 keV). He environment is not planned for 2015r1; this may follow an assessment of operations with the new detector and stages, depending on demand.
DPC: segmented photodiode detector for differential phase contrast in transmission. Can be used with either the ZP Nanoprobe or the KB microprobe.
*** DPC RECENTLY RECOMMISSIONED ***
Transmission: Ion chambers and photodiodes
On axis, in-line optical microscope with ~1-2 μm resolution, 700 μm field-of-view. Backside viewing only.
MODES OF OPERATION
SFXM Scanning Fluorescence X-ray Microscopy
2D elemental mapping of fluorescence emission in the range 1.6 keV to ~22 keV (Vortex detector) or 3.3 keV to 19.5 keV (Maia detector).
Micro-XANES - spatially resolved x-ray fluorescence near edge spectroscopy
Single point XANES from 4.2 keV to ~22 keV (Sc to Ru, and L-edges falling within this energy range) using the Vortex detector. Stack XANES / imaging XANES from 4.2 keV to 19.5 keV covering modest areas using the Maia detector.
High monochromaticity XANES (311 crystal) is available - potential users should contact David Paterson to discuss their proposed study.
STXM Scanning Transmission X-ray Microscopy
Fast transmission maps (absorption and differential phase contrast) with incident energy range from 4.2 keV to ~22 keV
Single-slice (2-D) or volumetric (3-D) tomography on the KB microprobe is well established - ultimate resolution around 2-5 μm. Specimen diameter must be small enough to avoid self-absorption (for a discussion of self absorption, see de Jonge & Vogt, Current Opinion in Structural Biology 20 (2010)). Typical specimen size is 150 μm diameter, up to 1-mm long.
High-resolution tomography (500 nm resolution likely) is possible on the ZP nanoprobe for highly concentrated elements.
Potential tomography users should contact Martin de Jonge to discuss their proposed study.
If your experiment requires other capabilities, please contact the beamline scientists prior to submitting your proposal.
Proposals that do not fit within these capabilities may still be considered for beamtime at the discretion of the PAC.
Please contact beamline scientists to discuss your particular sample mounting requirements.
Beamline Contact: firstname.lastname@example.org