canSAS-X - Revision history

Butler: /* Geosciences validation and round robin */

2018-12-11T16:55:25Z

Geosciences validation and round robin

← Older revision		Revision as of 16:55, 11 December 2018
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	== Geosciences validation and round robin ==		== Geosciences validation and round robin ==
	Paul Butler pointed out that a large fraction of the USANS proposals at NIST at least are geosciences related but that there seems to be a need and an interest to help validate geosciences methodologies. These are mostly based on surface area and pore volume analysis but suffer from a variety of issues, not the least of which is very strong scattering, often leading to multiple scattering. Sometimes these are addressed by trying to make thinner samples but there is concern about the effect of grinding the surface on the results obtained. Another method often employed is to crush the samples into a "powder" to avoid the potentially damaging effects of grinding, but this can create a lot of new surfaces which will scatter in their own right. Finally the analysis methods can differ. It is proposed that a set of simple model ~~geosamples~~ be produced in a variety of the standard forms and be measured as round robins and the data also analyzed in various ways by various people to explore the limits of technique. An Initial set of USAS instruments at NIST, ANSTO and Argone will be used. Others will be contacted in due time but anyone interested in participating immediately is welcome. Paul Butler (butlerpd@udel.edu) will try to co-ordinate this effort.		Paul Butler pointed out that a large fraction of the USANS proposals at NIST at least are geosciences related but that there seems to be a need and an interest to help validate geosciences methodologies. These are mostly based on surface area and pore volume analysis but suffer from a variety of issues, not the least of which is very strong scattering, often leading to multiple scattering. Sometimes these are addressed by trying to make thinner samples but there is concern about the effect of grinding the surface on the results obtained. Another method often employed is to crush the samples into a "powder" to avoid the potentially damaging effects of grinding, but this can create a lot of new surfaces which will scatter in their own right. Finally the analysis methods can differ.

			It is proposed that a set of simple model samples be produced, using synthetic and/or monomineralic rocks, in a variety of the standard forms (expect about 4) and see how much the results differ. In a next step one would proceed to more complex rocks such as granite and eventually shales.

			These should also be measured as round robins and the data also analyzed in various ways by various people to really explore the limits of technique. An Initial set of USAS instruments at NIST, ANSTO and Argone will be used. Others will be contacted in due time but anyone interested in participating immediately is welcome. Paul Butler (butlerpd@udel.edu) will try to co-ordinate this effort.

	The suggestion was also made that depending on how the project progresses, the outcomes could be useful to the new ISO effort on surface area.		The suggestion was also made that depending on how the project progresses, the outcomes could be useful to the new ISO effort on surface area.

Butler: /* NXcanSAS 2.0 */

2018-12-11T16:49:18Z

NXcanSAS 2.0

← Older revision		Revision as of 16:49, 11 December 2018
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	* On the other hand, from the point of view of the rapidly growing communities interested in data curation/databases, machine learning and automated data analysis tools, there is an urgent need to add specific tag definitions for common metadata in order for the utility of such a complete standard to be fulfilled. While the standard allows for any metadata to be included for an individual’s specific purpose, its utility is very limited without an agreement that all producers and consumers of the data can understand.		* On the other hand, from the point of view of the rapidly growing communities interested in data curation/databases, machine learning and automated data analysis tools, there is an urgent need to add specific tag definitions for common metadata in order for the utility of such a complete standard to be fulfilled. While the standard allows for any metadata to be included for an individual’s specific purpose, its utility is very limited without an agreement that all producers and consumers of the data can understand.

	As part of this last point, the interest ([[#Correlative Analysis and COST Action\| see software discussion below]]) in intensifying efforts to analyse and refine multiple data sets from different analytical techniques against each other, the question of handling multi-modal data sets and how to store them was raised. Of particular interest was the growing use of multiple techniques “simultaneously” at the beam line. Indeed a subject of some discussion was the fact that some measurements may be truly simultaneous while others may precede or follow the SAS measurement (e.g. inline chromatography) and how to distinguish between time-stamps vs time differentials. Some proposals were put forward. It was suggested these could be implemented within the current standard though it was not clear to everyone how that would work.		As part of this last point, the interest ([[#Correlative Analysis and COST Action\| see software discussion below]]) in intensifying efforts to analyse and refine multiple data sets from different analytical techniques against each other, the question of handling multi-modal data sets and how to store them was raised. Of particular interest was the growing use of multiple techniques “simultaneously” at the beam line. Indeed a subject of some discussion was the fact that some measurements may be truly simultaneous while others may precede or follow the SAS measurement (e.g. inline chromatography) and how to distinguish between time-stamps vs time differentials. Some proposals were put forward. It was suggested these could be implemented within the current standard though it was not clear to everyone how that would work. Some example use cases need to be developed to demonstrate. Furthermore, the consumers of the data (analysis software) would needed that understand the information and can handle plotting and resampling of such data.

Butler: /* ISO standards Development */

2018-12-11T16:45:19Z

ISO standards Development

← Older revision		Revision as of 16:45, 11 December 2018
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	Michael Krumery briefly described the ISO structure and processes and the status of its sas related activities. ISO is the international standards organization whose current membership includes 162 national standards bodies. At present there are 784 technical committees and subcommittees of which TC-24: particle characterisation including sieving is the one of intereste to SAS. He described how the standards go through a 3 year development track and are reviewed every 5 years. He discussed the current standard which is a technical standard that defines how to do a SAXS measurement to obtain the mean particle diameter (ISO 17867). Finally, he mentioned a new proposal to create a total surface area standard based on the SAXS invariant analysis.		Michael Krumery briefly described the ISO structure and processes and the status of its sas related activities. ISO is the international standards organization whose current membership includes 162 national standards bodies. At present there are 784 technical committees and subcommittees of which TC-24: particle characterisation including sieving is the one of intereste to SAS. He described how the standards go through a 3 year development track and are reviewed every 5 years. He discussed the current standard which is a technical standard that defines how to do a SAXS measurement to obtain the mean particle diameter (ISO 17867). Finally, he mentioned a new proposal to create a total surface area standard based on the SAXS invariant analysis.

	In the ensuing discussion it became clear that the creation of ISO standards require a lot of work are generally driven by industrial/commercial needs to for example be able to certify equipment and is not really suitable for academic use in for, for example, validating data to be published. While not impossible to extend to SANS officially, the commercial need case is hard to make. It was suggested that it might be interesting for SANS instruments to try to meet the standard informally. That said, canSAS activities could probably contribute information into the ISO process, for example through its round robin effort.		In the ensuing discussion it became clear that the creation of ISO standards require a lot of work are generally driven by industrial/commercial needs to for example be able to certify equipment and is not really suitable for academic use in for, for example, validating data to be published. While not impossible to extend to SANS officially, the commercial need case is hard to make. It was suggested that it might be interesting for SANS instruments to try to meet the standard informally. It should be noted that ISO standards are about process not standard samples. That said, canSAS activities could probably contribute information into the ISO process, for example through its round robin effort.

	== Geosciences validation and round robin ==		== Geosciences validation and round robin ==

Butler: /* canSAS-X Workshop */

2018-12-10T16:25:42Z

canSAS-X Workshop

← Older revision		Revision as of 16:25, 10 December 2018
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	== Geosciences validation and round robin ==		== Geosciences validation and round robin ==
	Paul Butler pointed out that a large fraction of the USANS proposals at NIST at least are geosciences related but that there seems to be a need and an interest ~~to work~~ to help ~~validated~~ geosciences methodologies. These are mostly based on surface area and pore volume analysis but suffer from a variety of issues, not the least of which is very strong scattering often leading to multiple scattering. Sometimes these are addressed by trying to make thinner samples but there is concern about the effect of grinding the surface on the results obtained. Another method often employed is to crush the samples into a "powder" to avoid the potentially damaging effects of grinding, but this can create a lot of new surfaces which will scatter in their own right. Finally the analysis methods can differ. It is proposed that a set of simple model geosamples be produced in a variety of the standard forms and be measured as round robins and the data also analyzed in various ways by various people to explore the limits of technique. An Initial set of USAS instruments at NIST, ANSTO and Argone be ~~tried~~. Others will be contacted in due time but anyone interested in participating immediately is welcome. Paul Butler (butlerpd@udel.edu) will try to co-ordinate this effort.		Paul Butler pointed out that a large fraction of the USANS proposals at NIST at least are geosciences related but that there seems to be a need and an interest to help validate geosciences methodologies. These are mostly based on surface area and pore volume analysis but suffer from a variety of issues, not the least of which is very strong scattering, often leading to multiple scattering. Sometimes these are addressed by trying to make thinner samples but there is concern about the effect of grinding the surface on the results obtained. Another method often employed is to crush the samples into a "powder" to avoid the potentially damaging effects of grinding, but this can create a lot of new surfaces which will scatter in their own right. Finally the analysis methods can differ. It is proposed that a set of simple model geosamples be produced in a variety of the standard forms and be measured as round robins and the data also analyzed in various ways by various people to explore the limits of technique. An Initial set of USAS instruments at NIST, ANSTO and Argone will be used. Others will be contacted in due time but anyone interested in participating immediately is welcome. Paul Butler (butlerpd@udel.edu) will try to co-ordinate this effort.

	The suggestion was also made that depending on how the project progresses, the outcomes could be useful to the new ISO effort on surface area.		The suggestion was also made that depending on how the project progresses, the outcomes could be useful to the new ISO effort on surface area.
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	Unfortunately, the proposal failed the first submission with the authors and proposers awaiting its review documentation. It is anticipated that, subject to revisions, it will be resubmitted within the next 12 months.		Unfortunately, the proposal failed the first submission with the authors and proposers awaiting its review documentation. It is anticipated that, subject to revisions, it will be resubmitted within the next 12 months.

			== Data and/or code repositories ==

			== Other opportunities (machine learning/MD simulations etc) ==

	=== Open Microphone Session ===		=== Open Microphone Session ===

Butler: /* Geosciences validation and round robin */

2018-12-10T16:19:24Z

Geosciences validation and round robin

← Older revision		Revision as of 16:19, 10 December 2018
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	== Geosciences validation and round robin ==		== Geosciences validation and round robin ==
	Paul Butler ~~made the case~~ that a large fraction of the USANS proposals at NIST are geosciences related but that there seems to be a need and an ~~intereste~~ to work to help validated geosciences methodologies. These are mostly based on surface area and pore volume analysis but ~~suffere~~ from a variety of issues, not the least of which is very strong scattering often leading to multiple scattering. Sometimes these are addressed by trying to make thinner samples but there is concern about ~~another~~ method ~~used~~ is powder but this can create a lot of new surfaces. Finally the analysis methods can ~~differe~~. It is proposed that a set of simple model geosamples be produced in a variety of the standard forms and be measured as round robins and the data also analyzed in various ways by ~~vairous~~ people to explore the limits of technique. An Initial set of ~~USANS~~ instruments at NIST, ANSTO and ~~USAXS at~~ Argone be tried. ~~Also ORNL and ILL USANS users are~~ interested in ~~helping~~. Paul Butler will try to co-ordinate.		Paul Butler pointed out that a large fraction of the USANS proposals at NIST at least are geosciences related but that there seems to be a need and an interest to work to help validated geosciences methodologies. These are mostly based on surface area and pore volume analysis but suffer from a variety of issues, not the least of which is very strong scattering often leading to multiple scattering. Sometimes these are addressed by trying to make thinner samples but there is concern about the effect of grinding the surface on the results obtained. Another method often employed is to crush the samples into a "powder" to avoid the potentially damaging effects of grinding, but this can create a lot of new surfaces which will scatter in their own right. Finally the analysis methods can differ. It is proposed that a set of simple model geosamples be produced in a variety of the standard forms and be measured as round robins and the data also analyzed in various ways by various people to explore the limits of technique. An Initial set of USAS instruments at NIST, ANSTO and Argone be tried. Others will be contacted in due time but anyone interested in participating immediately is welcome. Paul Butler (butlerpd@udel.edu) will try to co-ordinate this effort.

	The suggestion was also made that depending on how the project progresses, the ~~oucomes~~ could be useful to the new ISO effort on surface area ~~since that is in fact the heart of most geosciences scattering analysis~~.		The suggestion was also made that depending on how the project progresses, the outcomes could be useful to the new ISO effort on surface area.

	== Other Standard/round robin discussion ==		== Other Standard/round robin discussion ==

Butler: /* canSAS-X Workshop */

2018-12-10T14:29:59Z

canSAS-X Workshop

@@ Line 200: / Line 200: @@
 It was agreed that besides clarifying the current standard, the working group should develop some more challenging example use cases, and in particular how included extended data for multimodal data for example.  Moreover it was noted that it was time to “bite the bullet” and try to develop wrappers/converters to and from NXcanSAS and other formats
-=== Correlative Analysis and COST Action ===
+=== Reproducibility and Reliability: Standards and Round Robins ===
 In April 2018 a COST action was submitted under the title of ''Combining Everything: Developing Rigorous Pan Metrological Correlative Analyses (Pan-CORAL)''. The aim of this action was to bring together a network of people to work on a series of information optimisers, qualifying and quantifying data present in a given dataset and then bringing together this information from multiple data sources into a global optimiser to provide a ''top-level'' view of the information gathered about a sample. Conversely, ultimately, the system would also be able to propose suitable analyses to conduct on a sample, given input from a user about what it is they may want to quantify.

Butler: /* NXcanSAS 2.0 */

2018-12-10T14:27:29Z

NXcanSAS 2.0

← Older revision		Revision as of 14:27, 10 December 2018
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	=== NXcanSAS 2.0 ===		=== NXcanSAS 2.0 ===
	~~Following on from the ratification~~ of the NXcanSAS standard ~~since~~ the ~~last 'full'~~ canSAS meeting it was ~~decided~~ that the ~~primary focus~~ of ~~attention~~ for a 1.1 ~~or 2~~.~~0 revision would~~ be ~~focussed less on new functionality~~ and, ~~instead~~, ~~clarifying~~ the ~~existing standard as different facilities are now exporting NXcanSAS~~ data ~~with subtly different interpretations~~. ~~Therefore unification~~ of the standard~~, before building upon~~ it~~, appeared prudent~~.		[http://www.cansas.org/wgwiki/index.php/NXcanSAS\| After several years of work], the [http://download.nexusformat.org/doc/html/classes/applications/NXcanSAS.html\| NXcanSAS standard] was approved By the NeXus International Advisory Group (NIAG) in early 2017 and announced at the Berkeley [[canSAS-IX\| canSAS meeting]]. In the year since that announcement the status of implementation, the Diamond reduction software [https://dawnsci.org\| DAWN], the neutron package [http://www.mantidproject.org\| MANTID] used by a growing number of neutron sources, while the NIST IGOR based [https://www.ncnr.nist.gov/programs/sans/data/red_anal.html\| reduction macros] are in the process of implementing an NXcanSAS outputand. The APS IGOR based reduction [https://www.aps.anl.gov/Science/Scientific-Software/Nika/\| NIKA] and analysis [https://www.aps.anl.gov/Science/Scientific-Software/Irena\| IRENA] packages written by Jan Ilavsky have implemented both the reading and writing of their reduced data in the NXcanSAS format. Finally, on the purely analysis side, [www.sasview.org\| SasView] has implemented the reading of such files and [https://www.bornagainproject.org/\| Born Again] is considering its use. Finally, it was noted that NSLS II is starting to move away from data files in favor of databases. This however could easily be used to create NXcanSAS data on the fly as needed. Two themes however emerged in the ensuing discussion:
			* From the point of view of the producers and consumers of data, there is an urgent need for clarification of the spec, or at least a meeting to understand why the various versions implemented to date do not all seem to inter-operate. This may simply require some discussion and careful reading of the full specification or it could require adding some clarifying language to the current spec (which could require a version 1.1).
			* On the other hand, from the point of view of the rapidly growing communities interested in data curation/databases, machine learning and automated data analysis tools, there is an urgent need to add specific tag definitions for common metadata in order for the utility of such a complete standard to be fulfilled. While the standard allows for any metadata to be included for an individual’s specific purpose, its utility is very limited without an agreement that all producers and consumers of the data can understand.

			As part of this last point, the interest ([[#Correlative Analysis and COST Action\| see software discussion below]]) in intensifying efforts to analyse and refine multiple data sets from different analytical techniques against each other, the question of handling multi-modal data sets and how to store them was raised. Of particular interest was the growing use of multiple techniques “simultaneously” at the beam line. Indeed a subject of some discussion was the fact that some measurements may be truly simultaneous while others may precede or follow the SAS measurement (e.g. inline chromatography) and how to distinguish between time-stamps vs time differentials. Some proposals were put forward. It was suggested these could be implemented within the current standard though it was not clear to everyone how that would work.


	Additionally discussion was had about:		Additionally discussion was had about:
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	* Handling uncertainties, specifically highlighting scalers, dI and dQ datasets, and maintaining their provenance and propagation throughout correction, reduction and analysis		* Handling uncertainties, specifically highlighting scalers, dI and dQ datasets, and maintaining their provenance and propagation throughout correction, reduction and analysis

	* The ~~rising quantities~~ of ~~metadata and where it~~ should ~~live~~		* A key point made by the industrial participants was the need to ensure that the requirement for any metadata be kept to an absolute minimum. In particular the data and metadata need to be stored in separate files when dealing with data from proprietary measurements. The philosophy used in developing the current specification was discussed. This was to require an abosulte minimum, namely an I and a q, but allow for producers and consumers of data to communicate at as high a leve as desired by defining a variety of useful but optional tags. This should continue in the next iteration of the specification.

	* Handling multi-modal datasets within either:
	** One HDF container file - containing multiple, unique, entries conforming to their appropriate application definitions
	** Multiple HDF container files - either linked, or standalone, but retaining the ability to reference one another

	~~The last topic also raised interesting questions~~ and ~~possibilities regarding intensifying efforts~~ to ~~analyse~~ and ~~refine multiple datasets~~ from ~~different analytical techniques against each~~ other.		It was agreed that besides clarifying the current standard, the working group should develop some more challenging example use cases, and in particular how included extended data for multimodal data for example. Moreover it was noted that it was time to “bite the bullet” and try to develop wrappers/converters to and from NXcanSAS and other formats

	=== Correlative Analysis and COST Action ===		=== Correlative Analysis and COST Action ===

Butler: /* Update/discussion on canSAS-IX activities */

2018-11-22T16:40:12Z

Update/discussion on canSAS-IX activities

← Older revision		Revision as of 16:40, 22 November 2018
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	*** The paper on the topic Brian Pauw offered to spearhead was published last year: B. R. Pauw, A. J. Smith, T. Snow, N. J. Terrill, A. F. Thünemann, ''The modular SAXS data correction sequence for solids and dispersions'', Journal of Applied Crystallography, 50: 1800–1811 (2017), '''DOI: 10.1107/S1600576717015096'''. Tim Snow will be speaking about it later at this SAS2018 meeting.		*** The paper on the topic Brian Pauw offered to spearhead was published last year: B. R. Pauw, A. J. Smith, T. Snow, N. J. Terrill, A. F. Thünemann, ''The modular SAXS data correction sequence for solids and dispersions'', Journal of Applied Crystallography, 50: 1800–1811 (2017), '''DOI: 10.1107/S1600576717015096'''. Tim Snow will be speaking about it later at this SAS2018 meeting.
	** Data repository – including metadata *		** Data repository – including metadata *
			*** Brian Pauw has started a data repository at BAM and initiated a collaboration with Diamond. Work is ongoing.
			*** Chris Tissone (SLAC) and NSLS-II are also looking at this for Machine Learning purposes and have some local repos started.
			*** Could also think of adding data under scattering-central on github.
			*** At this point need some experimentation to find best approach(es)
	** Multiple scattering effects - warning and model fitting		** Multiple scattering effects - warning and model fitting
	*** The ideas presented by Grethe Jensen are now published (G. V. Jensen and J. G. Barker, ''Effects of multiple scattering encountered for various small-angle scattering model functions'', Journal of Applied Crystallography, '''51''', 1455-1466 (2018), doi:10.1107/S1600576718010816), while Henrich Freilinghaus is also working on a paper on the topic.		*** The ideas presented by Grethe Jensen are now published (G. V. Jensen and J. G. Barker, ''Effects of multiple scattering encountered for various small-angle scattering model functions'', Journal of Applied Crystallography, '''51''', 1455-1466 (2018), doi:10.1107/S1600576718010816), while Henrich Freilinghaus is also working on a paper on the topic.

Butler: /* canSAS XI meeting planning update */

2018-11-22T03:56:12Z

canSAS XI meeting planning update

← Older revision		Revision as of 03:56, 22 November 2018
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	=== canSAS XI meeting planning update ===		=== canSAS XI meeting planning update ===
	The location and arrangements for canSAS-XI were presented by Henrich Frielinghaus. [[media:canSAS_XI_presentation.pdf \| Slides]]		The location and arrangements for canSAS-XI were presented by Henrich Frielinghaus. [[media:canSAS_XI_presentation.pdf \| Slides]]
			The website is up and linked from the wiki. The Venue will be Freising (near Munich airport) July 8-10, 2019. The registration fee will be 250€ and include meals. A single large room has been reserved. However, given the discussoin on the benefit of having small groups to promote active discussion, Henrich will look into booking some smaller rooms which should be possible.

			Let Henrich know if people need an official invitation.

	=== NXcanSAS 2.0 ===		=== NXcanSAS 2.0 ===

Butler: /* Update/discussion on canSAS-IX activities */

2018-11-22T03:48:34Z

Update/discussion on canSAS-IX activities

← Older revision		Revision as of 03:48, 22 November 2018
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	* '''Reproducibility and Reliability'''		* '''Reproducibility and Reliability'''
	** New experimental calibration standards and round robin data collection. Including for GISANS and soft X-ray		** New experimental calibration standards and round robin data collection. Including for GISANS and soft X-ray
			*** Andy Smith has worked on a 100 nm Silicon Nitride calibration grating for SAXS. Data has been collected and it works (accuracy seems to be ~ 1%) however the gratings are rather fragile and the cost of manufacture is ~ 3500 GBP.
			**** Action: Andy to contact Silson out about possibility and cost of bulk order
			*** Joe Kline has followed up as promised by engaging the NIST nanofab which is currently working to produce platinum filled Silicon Oxide troughs and pillar, backed with nitride and polished. If successful the next step will be to produce randomly arranged pillars.
			*** Adrian update on nanocrystalline glasses: First set of samples were a bit too thick for x-rays. Some were sent around but been mislaid. In the meantime need to work on getting them thinner.
			**** Action: Adrian needs to get back to the company on thickness that can be produced
			*** The working group should continue working and set up protocols for using the standards developed.
	** Documentation of best practices for data collection and reduction		** Documentation of best practices for data collection and reduction
	*** The paper on the topic Brian Pauw offered to spearhead was published last year: B. R. Pauw, A. J. Smith, T. Snow, N. J. Terrill, A. F. Thünemann, ''The modular SAXS data correction sequence for solids and dispersions'', Journal of Applied Crystallography, 50: 1800–1811 (2017), '''DOI: 10.1107/S1600576717015096'''. Tim Snow will be speaking about it later at this SAS2018 meeting.		*** The paper on the topic Brian Pauw offered to spearhead was published last year: B. R. Pauw, A. J. Smith, T. Snow, N. J. Terrill, A. F. Thünemann, ''The modular SAXS data correction sequence for solids and dispersions'', Journal of Applied Crystallography, 50: 1800–1811 (2017), '''DOI: 10.1107/S1600576717015096'''. Tim Snow will be speaking about it later at this SAS2018 meeting.
	** Data repository – including metadata *		** Data repository – including metadata *
	** Multiple scattering effects - warning and model fitting		** Multiple scattering effects - warning and model fitting
	*** The ~~paper suggested~~ by Grethe Jensen is now ~~out~~ (G. V. Jensen and J. G. Barker, ''Effects of multiple scattering encountered for various small-angle scattering model functions'', Journal of Applied Crystallography, '''51''', 1455-1466 (2018), doi:10.1107/S1600576718010816), while Henrich Freilinghaus is also working on a paper.		*** The ideas presented by Grethe Jensen are now published (G. V. Jensen and J. G. Barker, ''Effects of multiple scattering encountered for various small-angle scattering model functions'', Journal of Applied Crystallography, '''51''', 1455-1466 (2018), doi:10.1107/S1600576718010816), while Henrich Freilinghaus is also working on a paper on the topic.
	*** Brian Pauw is working on data quality flags and Grethe is working with Paul Kienzle to incorporate multiple scattering into SasView. Henrich is also hoping to develop software tools.		*** Brian Pauw is working on data quality flags and Grethe is working with Paul Kienzle to incorporate multiple scattering into SasView. Henrich is also hoping to develop software tools.
	* '''Data Analysis and Emerging Techniques'''		* '''Data Analysis and Emerging Techniques'''