This appendix comprises the user documentation I wrote for the software to process the data from the curved image plate camera, as described in this project.
UCL
C L . R C
Curved Image Plate Camera
A new high-speed high-resolution X-ray diffraction facility, the Curved Image Plate camera, is now available at the synchrotron at Daresbury Laboratory. Relatively recent detector developments (image-plates), coupled with readily available computing power, have given new life to the Debye-Scherrer camera. This document outlines the capabilities and use o f the camera, and details operation o f the custom software.
Contents Introduction
Overview of the CIP system
Use of the image analysis (2D to ID conversion) programs o A) Basic operation: CIP Analysis
o B) Basic operation: Peaker
o Testing the calibration
o Further interpretation of the Error graph o Obtaining and maintaining accuracv in reality o Some Advanced features
o Summary o f software operation
Hints for running the experiment Further reading (background) Errata
Appendix I - file formats
Appendix H - typical scanner spatial characteristis
Introduction
The Curved Image Plate (CIP) system developed by UCL in conjimction with Daresbury Laboratory is a large X-ray diffraction camera with Debye-Scherrer geometry, utilising a storage-phosphor based image plate as the detector. Being a passive device, the image plate is used very much like photographic film, but is many times more sensitive, has a largely linear response to X-ray intensity, and its latent image may be read into a computer by an optical scanner immediately after exposure.
In contrast to conventional diffractometers, the CEP system offers data collection times up to an order of magnitude quicker, enabling high-resolution time- and
temperature-resolved studies. [At present an Oxford Cryostream is used to study samples at temperatures down to 77K, and a furnace suitable for the 200°C to 800°C region is available. Time resolution is of order of minutes.] A precision in 2-theta of ±0.01° is typical, but with care and frequent calibration, up to ±0.002° can be realised. With 0.5mm capillary tubes the system can resolve peaks as close as 0.07°, and is also particularly suited to the study of amorphous materials.
To cater for different requirements there are two cameras, with radii of 350 and 185mm. Both are used with 400x150mm images plates, covering 0 to 64° on the large arc and 0 to 120° on the small. The large arc lends itself to high-resolution crystal work, while the small arc is more suited to amorphous studies because of its larger Q-range and the greater intrinsic intensity obtained. Wavelengths between 0.4 and 1.0Â are used - harmonics from the silicon double-bounce monochromator can become a problem at longer wavelengths.
Overview of the CIP system
On Wiggler beamline 9.1 at Daresbury, exposures ranging from 5minutes (crystalline,
(30s of typical room lighting will erase 90% of the signal). Plates can be scanned at two resolutions, with pixel sizes o f 176pm or 88pm. ImageQuant software on the reader is used to initialise the scan which takes Sminutes for low-resolution scans or about 18minutes for high. The image is displayed on the screen after scanning and simple spot-checks can be performed at that stage.
ImageQuant outputs a gel file, w^ich is essentially a two-dimensional dataset of the image fi-om the phosphor screen. In general though, for analysis of amorphous or powder data, a one-dimensional dataset of scattered intensity versus 2-theta (or d, or Q) is required. This form may be an end result in itself or may be used as the starting point for more advanced techniques such as structure refinement.
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A trivial means of obtaining an intensity versus 2-theta plot would be to sample the intensity of the image along a sufficiently narrow strip down its vertical centre (the principal scattering plane). The major limitation o f this approach is the complete wastage of data from a large portion of the image.
Given the geometrical arrangement of the camera, it is possible for a computer program
on a pixel-by-pixel basis. By using data from the whole of the plate the best signal-to-noise ratio is achieved and data-collection times can be minimised. Software is provided for performing this numerical integration.
Experienced users should note that significant revisions and bug-fixes were made to the software in January 2000.
In particular, the file formats were changed to allow 'processing history' to be recorded. Old-style files can still be read and written by the current software versions, if required. In CIP Analysis, 'skew strip'- and 'psi-limited'-integration options were introduced.
Use o f the image analysis (2D to ID conversion)
programs
These programs perform the numerical integration and camera-calibration procedures. At present, there are four distinct units:
• CIP Analysis - which reads gel files, performs integration around the rings, then outputs linegraphs (ID datasets).
• Peaker - an accessory to the above - which reads the ID datasets, constructs an on-screen graph, and identifies peak-positions. The location of peaks measured from calibration samples (typically silicon) can be compared with their corresponding theoretical positions. When correctly interpreted, the resulting "error-graph" highlights any wavelength discrepancy, or sample mis-alignment error, and may be used to generate calibration curves (then used in CIP Analysis
for subsequent datasets to correct for the misalignment).
• ScannerCal - an accessory which is used to create spatial-calibrations for the image-plate scanner.
• GEL Indexer - an accessory which builds an index file of all gel files in a directory, using the sample description fields.
A) Basic operation: CIP Analysis 1. Start CIP Analysis.
2. Go to File|Open, and load a silicon calibration run. After the image has loaded, a box appears containing the description given to the data when it was scanned, the Researcher and date (if filled in at scan-time), and the image size and scan
4. Observe how the "XRD info." box indicates the current position of the mouse pointer on the image, and intensity at that point. This box also contains a scroller which adjusts the brightness of the image as it appears on the screen. Move it rightwards for more brightness - the new setting takes a few seconds to come into effect.
5. Initially, the left mouse button is configured to set the direct beam position: use the scrollbars to bring the direct beamspot into view, then carefully position the mouse cross-hairs pointer over it and click the left button. A set of larger green cross-hairs appears over the selected beam-origin. If required, the arrow-keys on the keyboard can be used to "nudge" the position of the cross-hairs.
6. Now select the area over which to integrate: click the right mouse button over the image to summon the pop-up menu and choose "Select integration area". The cursor will change to a box with comer cross-hairs, and remains in "box mode" until selected otherwise. Position the mouse in one comer of the box you wish to select and left-click the mouse (atpresent there is no visual confirmation that anything has happened). Now move to the diagonally opposite comer (scrolling the window if required) and click again. A blue rectangle shows the selected region. [Note: the box has to have an area of at least 36 pixels.]
7. Once the direct beam and the box have been selected, click "Integrate" on the application's menu. You will be presented with the pre-integration dialog box.
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8. Select the arc radius of the camera and enter the X-ray wavelength used for the image. [The wavelength is used to calculate the d-spacings and Q-values and is saved to file later]. Leave all the other options unchecked or in their default state for now.
9. Click the "Integrate" button to begin integration. On a fast computer this will take at most a few seconds, and the time taken is roughly proportional to the area of the region integrated over. A pop-up box shows the progress.
10. When the integration is complete, a red line-graph is superimposed down the left side of the image. A visual check should show that the peaks align with the rings in the image, and are reasonably symmetrical. [The most likely cause of asymmetric peaks is selection of the wrong arc-radius].
11. The linegraph (ID dataset) can be saved [File|Save as...] in one of two formats: " ixd" or "Daresbury PDS". The former is the native format, and should always be used. It is simply an informative header followed by columnar 2-theta, d, Q, intensity, and is used by Peaker to set up calibrations etc. This format is also easily imported by other applications on PCs [e.g. Excel] or UNIX.
12. Go to File|Save as ixd... - the default filename is derived from the gel filename. IMPORTANT: the "intensity" output by the program represents the
intensity-per-unit-length of Debye-Scherrer ring, as measured in the principal scattering plane (narrow central vertical strip). The intensities are effectively what you would get as raw data from a conventional 2-theta diffractometer, and are NOT adjusted to
total-energy-in-ring or multiplied by any Lorentz factor.
B) Basic operation: Peaker
should appear on the screen, with an empirical background fit in red, and the peaks marked in blue.
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3. To zoom in, click and hold the (left) mouse button in one comer or the area you wish to zoom in on, then drag the mouse to the diagonally-opposite comer (visual feedback is in the form of a dotted box). The other (right) mouse button can be clicked to zoom out again.
4. Go to File|Open D-reference... and load the calibration file (e.g. silicon.rpp), entering the wavelength used for your data when prompted. A set of green reference marks will be displayed at the lx)ttom of the gr^h.
Now go to Comparison|Compare - provided the experimental lines are not too far out, they will be paired up with the appropriate theoretical lines. A calibration graph [(measured peak-position)-(theoretical position)] will be displayed in Peaker’s second window. A smooth curve (2nd order polynomial) is fitted to the graph.
their correct positions. In practice, it often isn't! In this example there will probably be quite a strong slope, since no scanner calibration was specified (on the Phosphorlmager 400 the 176/88pm quoted resolutions are only nominal, and the real average pixel-size is likely to be half a percent off that figure).
You have now completed a quick mn-through of the basic features of the software. Calibrations can be applied to obtain more accurate results, but before delving into the application of corrections, it is worth investigating the causes of the errors.
Causes of errors
When analysing the cause o f errors it is important to appreciate the scale of the relation between linear distance on the image plate and the 2-theta equivalent, given that we aim to achieve accuracies better than ±0.01°.
a d t fat ^ equivalent delta 2theta
1 ** * * 1 large arc (R=35bmm) l[ small arc (R=185mm) |
1 88pm 0.014° II 0.027°
176pm 0.028° i| 0.055°
1 1mm 0.16° l| 0.31°
Naturally the camera is highly sensitive to many forms of spatial misalignments, and especially so with the small arc.
The principal problem at the camera is locating the capillary at the geometric centre of the arc. Any misalignment immediately translates to an error in 2-theta (see the table above for an indication of magnitude) which varies with angle.
Distortions in the Phosphorlmager 400 scanner are a major contributor to the overall error. Across the short side of the plate pixels are slightly non-uniformly distributed, sometimes lying as far as 300pm from where you'd expect based on a linear scale. Along the long side of the plate, owing to the limitations of the mechanical design of the scanner, the scale expands and contracts periodically, with some rows of pixels up to 150pm from where you'd expect. This anomaly causes the characteristic four ripples seen in the error graph above. Accuracy of rings at higher 2-theta is mainly governed by the y-error (longitudinal), while for low-angle rings (coupled with a wide integration
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Calibrations
Distortions in the scanner can be quantified by scanning an image plate which has been exposed through a special mask having holes on a fine regular square grid.
Essentially we wish to measure the location of the dots in the image so that, knowing they originated as a 2mm x 2mm grid, the scale and distortions can be deduced. The design of the scanner is such that the x- and y-distortions can be assumed independent. To reduce random errors in the measurement o f spot position and to overcome quantisation errors, we want to locate the average horizontal (or vertical) positions of spots fi"om several lines (columns).
An option in CIP Analysis allows "integration" purely horizontally or vertically. Clicking CalibrationjGrid x-calib creates a file of average intensity against x-coordinate for all the pixels within the integration area. Similarly, Grid y-calib generates intensity against y-coordinate.
By peak-finding on these files, the spots are located. From the spot locations a lookup table is generated referencing pixel position to true position.
Creating a grid-calibration
1. Expose and scan a 'grid'. Place the Kodak plate (permanently fixed to an aliuninium backing) on a level surface, lay the grid mask over it and weigh down the comers using four lead bricks, padded by the foam supplied. Turn off the room lights, and expose the plate to the light fi-om the shortwave UV torch for about 6
Note; when used as directed, the UV light poses no significant risk to human health, however you should take care not to look directly at the UV tube, or direct
dots, and tall enough to catch 10 to 20 rows of spots. If some of the spots on the image plate are blurred for any reason, try to avoid these regions and select a band containing only well defined spots. Go to Calibration|Save grid x-calib and enter a filename (or accept the default). This procedure averages the intensity in vertical rows of pixels and outputs a datafile of average intensity against x-coordinate. 4. Repeat step 3, but for the y-calibration. Draw a vertical box the full height of the
grid, and about 10 to 20 spots wide. Use Calibration|Save grid y-calib. Again, try to avoid any blurry regions.
5. Open the x-calibration file using Peaker You should see a "hedgehog" graph, with regular spikes due to each column of spots. Check that there are no missed peaks, and that there are no "extra"peaks identified by the program. Select File|Save peak-positions. This saves a file containing the x-coordinates of the peaks (extension pks).
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6. Repeat step 5, but for the y-calibration file.
7. Lastly, the ScannerCal program is used to process the two files o f peak-positions into die final calibration lookup file.
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8. Use the [Open X file], and [Open Y file] buttons to select the peaks files. With the new file-formats in place since January 2000, the other parameters boxes should fill themselves in. \I f using oldfiles, you have to manusJly enter the resolution of the scan (176/88|im), and the width and height, in pixels, of the whole image. For a whole plate scan (£2-121 in ImageQuant), 176pm scans are 896 by 2280, wfiile 88pm scans are 1664 by 4560. If you have used any other scan size, you should, of course, enter the actual size of your grid-image. When open in CIP Analysis, an image's size can be found by selecting File|Information ]
9. Click the [Create Calibration file] button when you are ready. Again, when using the new files, a default filename will be suggested. [With the old software/files you will need to choose a filename of your own ]
Testing the calibration
1. Return to CIP Analysis, and open the gel file for a silicon run taken near the same time as the grid.
2. Proceed as in A) Basic operation: CIP Analysis to set up an integration, but additionally, at stage 8, press the [Change] button next to "apply scanner calibration" in the Integration dialog box, and select the calibration file you just created.
3. Save the ixd file as before.
4. Load the file in Peaker, and repeat the comparison with the silicon reference file. 5. The error-graph should be much smoother, showing practically none of the
oscillations that were present before.
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Further interpretation of the Error graph
If there is a zero error, that is, the trend misses the origin by much more than one pixel [e.g., 0.03° for a 176pm large-arc scan] then your specified beam origin could be slightly inaccurate. Try to ensure the cross-hair beam position in CIP Analysis was placed correct to the nearest pixel. Don't forget the arrow-keys can be used to fine-tune the position of the cross-hairs.
A major curve (like a quarter of a sine-wave) in the graph is almost invariably symptomatic o f a misplacement of the capillary relative to the arc of the camera. For the large arc, the capillary should be 349±lmm (small arc; 184mm) upstream fi-om the inside surface of the black polycarbonate near the beam-stop. 1mm of sample movement makes a very appreciable difference, at 50° creating an error of 0.2° on the small arc or 0.1° on the large arc. If the trend takes the graph beyond ±0.1° then the problem is particularly serious, and must be investigated and eradicated before more data is taken.
(a) (b) (0 (4
Error graph shapes corresponding to sample (a) too far upstream, (b) too far downstream, (c) too high (camera too low), (d) too low (camera too high).
If the x-ray beam goes right through the middle of the beam-tubes, this fixes the height of the sample relative to the camera, and the height-error should be minimal.
A common effect is that the graph has a linear positive slope (/). This is a linear scaling error caused by the compression of the phosphor-side of the image plate when shaped into a curve in the camera. It regains its nominal size when flattened for scanning. A linear slope from the origin up to around 0.1° at 60° for the large arc is typical, and will