Background - Revision history

KevinYager: /* See Also */

2017-12-01T15:30:40Z

‎See Also

KevinYager: /* See Also */

2017-12-01T15:30:09Z

‎See Also

KevinYager at 17:14, 8 July 2015

2015-07-08T17:14:08Z

KevinYager: /* Sources */

2014-10-30T13:03:12Z

‎Sources

KevinYager: /* Sources */

2014-10-14T14:39:53Z

‎Sources

KevinYager: /* Sources */

2014-10-14T14:39:07Z

‎Sources

130.199.3.165: /* Sources */

2014-06-20T19:35:24Z

‎Sources

KevinYager: /* Local background */

2014-06-18T14:34:20Z

‎Local background

KevinYager: /* Full background subtraction */

2014-06-18T14:29:53Z

‎Full background subtraction

KevinYager at 14:26, 18 June 2014

2014-06-18T14:26:59Z

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 ==See Also==
 * J. G. Barker and D. F. R. Mildner [http://scripts.iucr.org/cgi-bin/paper?ks5470 Survey of background scattering from materials found in small-angle neutron scattering] ''J. Appl. Cryst.'' '''2015''', 48. [http://dx.doi.org/10.1107/S1600576715010729 doi: 10.1107/S1600576715010729]
-* B. R. Pauw, A. J. Smith, T. Snow, N. J. Terrill and A. F. Thünemann [http://scripts.iucr.org/cgi-bin/paper?vg5075 The modular small-angle X-ray scattering data correction sequence\ ''J. Appl. Cryst.'' '''2017''', 50, 1800-1811. [https://doi.org/10.1107/S1600576717015096 doi: 10.1107/S1600576717015096]
+* [[Data Correction]]

← Older revision		Revision as of 15:30, 1 December 2017
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	==See Also==		==See Also==
	* J. G. Barker and D. F. R. Mildner [http://scripts.iucr.org/cgi-bin/paper?ks5470 Survey of background scattering from materials found in small-angle neutron scattering] ''J. Appl. Cryst.'' '''2015''', 48. [http://dx.doi.org/10.1107/S1600576715010729 doi: 10.1107/S1600576715010729]		* J. G. Barker and D. F. R. Mildner [http://scripts.iucr.org/cgi-bin/paper?ks5470 Survey of background scattering from materials found in small-angle neutron scattering] ''J. Appl. Cryst.'' '''2015''', 48. [http://dx.doi.org/10.1107/S1600576715010729 doi: 10.1107/S1600576715010729]
		+	* B. R. Pauw, A. J. Smith, T. Snow, N. J. Terrill and A. F. Thünemann [http://scripts.iucr.org/cgi-bin/paper?vg5075 The modular small-angle X-ray scattering data correction sequence\ ''J. Appl. Cryst.'' '''2017''', 50, 1800-1811. [https://doi.org/10.1107/S1600576717015096 doi: 10.1107/S1600576717015096]

← Older revision		Revision as of 17:14, 8 July 2015
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	Subtracting a local background inherently includes all sources of background scattering noted above. This works well for well-defined structural peaks, where the contributions from the peak and the baseline can be easily identified. For diffuse scattering or even broad halos, this may not be possible.		Subtracting a local background inherently includes all sources of background scattering noted above. This works well for well-defined structural peaks, where the contributions from the peak and the baseline can be easily identified. For diffuse scattering or even broad halos, this may not be possible.
		+
		+	==See Also==
		+	* J. G. Barker and D. F. R. Mildner [http://scripts.iucr.org/cgi-bin/paper?ks5470 Survey of background scattering from materials found in small-angle neutron scattering] ''J. Appl. Cryst.'' '''2015''', 48. [http://dx.doi.org/10.1107/S1600576715010729 doi: 10.1107/S1600576715010729]

@@ Line 2: / Line 2: @@
 ==Sources==
-# '''Detector''': Every detector has some background signal. The detector background may also have multiple components: a component that is present in every exposure (e.g. readout noise), as well as a component that scales with the exposure time (e.g. dark current). Detectors may also exhibit signals from other sources: e.g. cosmic rays, or even ambient light.
+# '''Detector''': Every [[detector]] has some background signal. The detector background may also have multiple components: a component that is present in every exposure (e.g. readout noise), as well as a component that scales with the exposure time (e.g. dark current). Detectors may also exhibit signals from other sources: e.g. cosmic rays, or even ambient light.
 # '''Air scattering''': The incident beam, and scattered rays, will be scattered by ambient air that they travel through. This tends to broaden the beams (and thus peaks), and introduces diffuse background into the measurement. This source of background can be minimized by flushing the beam path with [[Material:Helium|helium]] gas (which has very weak scattering), or by pumping-down to near [[Material:Vacuum|vacuum]]. Air scattering is most pronounced at lower [[x-ray energy|x-ray energies]]; it is nearly invisible for high-energy x-rays.
 # '''Instrumental''': Most x-ray instruments will have windows that isolate the x-ray source (which is under vacuum) from the sample chamber. Even if the sample chamber is evacuated, x-ray transparent windows will likely remain in place. These windows (although nominally x-ray transparent) will give rise to a scattering signal. This scattering can be partially blocked using guard slits downstream of the window (ideally placed close to the sample). Even so, the low-''q'' scattering cannot be eliminated. Moreover, the slits will introduce some signal of their own (weak scattering; or bright streaks if they cut deeply into the incident beam). Windows placed after the sample (e.g. when the sample is in air but the downstream path is evacuated) will lead to scattering that cannot be eliminated. [[Material:Kapton|Kapton]] is frequently used; this material introduces diffuse low-''q'' scattering, as well as some weak halos at intermediate-''q''.

@@ Line 3: / Line 3: @@
 ==Sources==
 # '''Detector''': Every detector has some background signal. The detector background may also have multiple components: a component that is present in every exposure (e.g. readout noise), as well as a component that scales with the exposure time (e.g. dark current). Detectors may also exhibit signals from other sources: e.g. cosmic rays, or even ambient light.
-# '''Air scattering''': The incident beam, and scattered rays, will be scattered by ambient air that they travel through. This tends to broaden the beams (and thus peaks), and introduces diffuse background into the measurement. This source of background can be minimized by flushing the beam path with [[Material:Helium|helium]] gas (which has very weak scattering), or by pumping-down to near vacuum. Air scattering is most pronounced at lower [[x-ray energy|x-ray energies]]; it is nearly invisible for high-energy x-rays.
+# '''Air scattering''': The incident beam, and scattered rays, will be scattered by ambient air that they travel through. This tends to broaden the beams (and thus peaks), and introduces diffuse background into the measurement. This source of background can be minimized by flushing the beam path with [[Material:Helium|helium]] gas (which has very weak scattering), or by pumping-down to near [[Material:Vacuum|vacuum]]. Air scattering is most pronounced at lower [[x-ray energy|x-ray energies]]; it is nearly invisible for high-energy x-rays.
 # '''Instrumental''': Most x-ray instruments will have windows that isolate the x-ray source (which is under vacuum) from the sample chamber. Even if the sample chamber is evacuated, x-ray transparent windows will likely remain in place. These windows (although nominally x-ray transparent) will give rise to a scattering signal. This scattering can be partially blocked using guard slits downstream of the window (ideally placed close to the sample). Even so, the low-''q'' scattering cannot be eliminated. Moreover, the slits will introduce some signal of their own (weak scattering; or bright streaks if they cut deeply into the incident beam). Windows placed after the sample (e.g. when the sample is in air but the downstream path is evacuated) will lead to scattering that cannot be eliminated. [[Material:Kapton|Kapton]] is frequently used; this material introduces diffuse low-''q'' scattering, as well as some weak halos at intermediate-''q''.
 # '''Sample holder''': Especially in transmission-scattering experiments, the sample will typically be contained in a holder (e.g. a capillary, or between two Kapton sheets). This holder will of course introduce scattering.

@@ Line 3: / Line 3: @@
 ==Sources==
 # '''Detector''': Every detector has some background signal. The detector background may also have multiple components: a component that is present in every exposure (e.g. readout noise), as well as a component that scales with the exposure time (e.g. dark current). Detectors may also exhibit signal arises from other sources: e.g. cosmic rays, or even ambient light.
-# '''Air scattering''': The incident beam, and scattered rays, will be scattered by ambient air that they travel through. This tends to broaden the beams (and thus peaks), and introduces diffuse background into the measurement. This source of background can be minimized by flushing the beam path with Argon gas (which has very weak scattering), or by pumping-down to near vacuum. Air scattering is most pronounced at lower [[x-ray energy|x-ray energies]]; it is nearly invisible for high-energy x-rays.
+# '''Air scattering''': The incident beam, and scattered rays, will be scattered by ambient air that they travel through. This tends to broaden the beams (and thus peaks), and introduces diffuse background into the measurement. This source of background can be minimized by flushing the beam path with [[Material:Helium|helium]] gas (which has very weak scattering), or by pumping-down to near vacuum. Air scattering is most pronounced at lower [[x-ray energy|x-ray energies]]; it is nearly invisible for high-energy x-rays.
 # '''Instrumental''': Most x-ray instruments will have windows that isolate the x-ray source (which is under vacuum) from the sample chamber. Even if the sample chamber is evacuated, x-ray transparent windows will likely remain in place. These windows (although nominally x-ray transparent) will give rise to a scattering signal. This scattering can be partially blocked using guard slits downstream of the window (ideally placed close to the sample). Even so, the low-''q'' scattering cannot be eliminated. Moreover, the slits will introduce some signal of their own (weak scattering; or bright streaks if they cut deeply into the incident beam). Windows placed after the sample (e.g. when the sample is in air but the downstream path is evacuated) will lead to scattering that cannot be eliminated. [[Material:Kapton|Kapton]] is frequently used; this material introduces diffuse low-''q'' scattering, as well as some weak halos at intermediate-''q''.
 # '''Sample holder''': Especially in transmission-scattering experiments, the sample will typically be contained in a holder (e.g. a capillary, or between two Kapton sheets). This holder will of course introduce scattering.
 # '''Matrix''': For materials that are dispersed (e.g. particles in solution or dispersed in a polymer), the matrix itself will lead to scattering.
 # '''[[Diffuse scattering]]''': Confusingly, sometimes the diffuse scattering arising from the sample may also be referred to as a kind of background. The diffuse scattering generally arises from disorder: it may be considered an unwanted background when analyzing a structural peak; but it may be the signal of interest when analyzing heterogeneous ordering.
 ==Measuring==
 One can attempt to measure the background, in preparation for subtracting it from the experimental data. A variety of measurements can be combined to assess the various sources of background.

@@ Line 35: / Line 35: @@
 # The distinct [[dynamical scattering]] features of GISAXS ([[Yoneda]] streak, [[specular rod]], [[reflectivity oscillations]], etc.) are all influenced by the complete multi-layer stack (by the film/substrate density profile in the normal direction). Since these features are different in the background and sample measurements, a direct subtraction is not meaningful.
 # The low-''q'' [[diffuse scattering]] is influenced by the roughness of interfaces (and scaled by the electron-density contrast across said interfaces). This is another example wherein the scattering of the substrate will be strongly modified by the presence of the sample film on top.
-Thus, although one can subtract the detector and direct-beam backgrounds, one cannot hope to subtract the 'empty cell' (substrate) background; this latter background is likely to be dominant. An alternative strategy is to instead subtract a 'local background' when extracting a [[Tutorial:Linecuts|linecut]].
+Thus, although one can subtract the detector and direct-beam backgrounds, one cannot hope to subtract the 'empty cell' (substrate) background; this latter background is likely to be dominant. An alternative strategy is to instead subtract a 'local background' when extracting a [[Tutorial:Linecuts|linecut]]. For instance, if assessing a peak position/width, one can fit the local data to a 'Gaussian + linear baseline' (or 'Gaussian + power-law baseline'), where the baseline is an (ad-hoc) accounting of the background. This inherently includes all the sources of background noted above.

@@ Line 26: / Line 26: @@
 I_{\mathrm{true}} = \frac{ (I_{\mathrm{sample}} - I_{\mathrm{readout}})/\int \mathrm{flux}_{\mathrm{sample}} \mathrm{d}t }{ (I_{\mathrm{background}} - I_{\mathrm{readout}})/\int \mathrm{flux}_{\mathrm{background}} \mathrm{d}t }
 </math>
 ===Local background===

@@ Line 4: / Line 4: @@
 # '''Detector''': Every detector has some background signal. The detector background may also have multiple components: a component that is present in every exposure (e.g. readout noise), as well as a component that scales with the exposure time (e.g. dark current). Detectors may also exhibit signal arises from other sources: e.g. cosmic rays, or even ambient light.
 # '''Air scattering''': The incident beam, and scattered rays, will be scattered by ambient air that they travel through. This tends to broaden the beams (and thus peaks), and introduces diffuse background into the measurement. This source of background can be minimized by flushing the beam path with Argon gas (which has very weak scattering), or by pumping-down to near vacuum. Air scattering is most pronounced at lower [[x-ray energy|x-ray energies]]; it is nearly invisible for high-energy x-rays.
-# '''Instrument windows''': Most x-ray instruments will have windows that isolate the x-ray source (which is under vacuum) from the sample chamber. Even if the sample chamber is evacuated, x-ray transparent windows will likely remain in place. These windows (although nominally x-ray transparent) will give rise to a scattering signal. This scattering can be blocked using guard slits downstream of the window (ideally placed close to the sample). Even so, the low-''q'' scattering cannot be eliminated. Windows placed after the sample (e.g. when the sample is in air but the downstream path is evacuated) will lead to scattering that cannot be eliminated. [[Material:Kapton|Kapton]] is frequently used; this material introduces diffuse low-''q'' scattering, as well as some weak halos at intermediate-''q''.
+# '''Instrumental''': Most x-ray instruments will have windows that isolate the x-ray source (which is under vacuum) from the sample chamber. Even if the sample chamber is evacuated, x-ray transparent windows will likely remain in place. These windows (although nominally x-ray transparent) will give rise to a scattering signal. This scattering can be partially blocked using guard slits downstream of the window (ideally placed close to the sample). Even so, the low-''q'' scattering cannot be eliminated. Moreover, the slits will introduce some signal of their own (weak scattering; or bright streaks if they cut deeply into the incident beam). Windows placed after the sample (e.g. when the sample is in air but the downstream path is evacuated) will lead to scattering that cannot be eliminated. [[Material:Kapton|Kapton]] is frequently used; this material introduces diffuse low-''q'' scattering, as well as some weak halos at intermediate-''q''.
 # '''Sample holder''': Especially in transmission-scattering experiments, the sample will typically be contained in a holder (e.g. a capillary, or between two Kapton sheets). This holder will of course introduce scattering.
 # '''Matrix''': For materials that are dispersed (e.g. particles in solution or dispersed in a polymer), the matrix itself will lead to scattering.
@@ Line 11: / Line 11: @@
 One can attempt to measure the background, in preparation for subtracting it from the experimental data. A variety of measurements can be combined to assess the various sources of background.
 * '''Dark signal''': By performing an exposure with the x-ray beam blocked, one can independently measure the '''detector''' component (#1) of the background.
-* '''Direct beam''': By performing an exposure with the x-ray beam turned on, but without any sample (or even sample cell), one can measure the contributions from '''detector''', '''air scattering''', and '''instrument windows''' (#1-3). The instrumental component can then be obtained by subtracting the dark signal from this direct beam measurement.
+* '''Direct beam''': By performing an exposure with the x-ray beam turned on, but without any sample (or even sample cell), one can measure the contributions from '''detector''', '''air scattering''', and '''instrumental''' (#1-3). The air+instrumental component can then be obtained by subtracting the dark signal from this direct beam measurement.
 * '''Empty cell''': By measuring the empty sample cell, one additionally includes the '''sample holder'''; i.e. one measures #1-4.
 * '''Empty cell (w/ matrix)''': One can instead measure an 'empty cell' where the '''matrix''' (e.g. solvent) is present; i.e. one measures #1-5.
@@ Line 18: / Line 18: @@
 ===Full background subtraction===
 In order to remove the effect of the background, the simplest solution is to simply measure it, and subtract it from the experimental data. However, there are a few issues to consider:
-* '''Exposure time''': Most of the sources of background scale with exposure time. So a valid subtraction will require using the same exposure time for the background and sample measurements. In principle, one can do a more general background subtraction by rescaling the background and sample measurements by the exposure time; however if the detector has readout noise (which doesn't scale with exposure time), then this procedure is not valid. In such a case, one should get a separate measure of the readout noise, and first subtract this from both images.
+* '''Exposure time''': Most of the sources of background scale with exposure time. So a valid subtraction will require using the same exposure time for the background and sample measurements. In principle, one can do a more general background subtraction by rescaling the background and sample measurements by the exposure time; however if the detector has readout noise (which doesn't scale with exposure time), then this procedure is not valid. In such a case, one should get a separate measure of the readout noise ('''dark signal'''), and first subtract this from both images.
 :<math>
 I_{\mathrm{true}} = \frac{ (I_{\mathrm{sample}} - I_{\mathrm{readout}})/t_{\mathrm{sample}} }{ (I_{\mathrm{background}} - I_{\mathrm{readout}})/t_{\mathrm{background}} }