canSAS - User contributions [en]

Tomography Working Group

2022-11-17T14:25:20Z

Tim.snow:

Placeholder for a small angle scattering tomography working group.

===Members===
* Tim Snow (DLS)
* Andre Conceicao (DESY)

===News/Status===
* 2022-11-17 - Working group mooted

===Subgroups===
* Tensor Tomography
* SANS Tomography

[[Category:Working Groups]]

Tomography Working Group

2022-11-17T14:19:46Z

Tim.snow: A working group for small angle scattering tomography endeavours

Placeholder for a small angle scattering tomography working group.

canSAS-X

2018-11-01T16:27:12Z

Tim.snow: /* Report on the Meeting */

= canSAS-X Workshop =

* date: Sunday, October 7, 2018
* place: Peninsula Room C, Grand Traverse Resort & Spa, Traverse City, Michigan, USA
* (just before [https://sas2018.anl.gov/ SAS2018])

__TOC__

== Background ==
canSAS (Collective Action for Nomadic Small Angle Scatters) workshops and activities are self assembled/bootstrap efforts to provide a forum for SAS users and providers to come together to discuss common needs and issues, to learn from each others experiences, discuss current best practices, hear about emerging techniques, and importantly to identify areas where the field/state of the art could be improved by bringing together the people that are interested and able to work cooperatively to solve the problem (see [[canSAS-IX#Goals]]).

As of [[canSAS-VIII | canSAS VIII]] in Tokai, Japan, the goal is to have a full independent workshop every three years, half way between the triennial SAS meetings, followed by some kind of forum at the SAS meetings themselves. These last have ranged in form from a half day session to just a lunch session to disseminate the status of activities. The intention is that the work agreed upon to solve current common problems will take place in the intervals between meetings, either at focused targeted workshops (see [[canSAS-2012]]), at ad-hoc gatherings of self-assembled working groups in person, or remotely.

At SAS2018 the organizers have arranged for space for sattelites the days prior and subsequent to the meeting proper and provided canSAS a day long block prior to the meeting itself.

== Goals ==

The goals for this one-day workshop are to get a status report on activities kicked off at [[canSAS-IX | canSAS IX]] and since, prepare for the next full, free standing [[canSAS-XI | canSAS workshop]] to be held in Freising, Germany from 8 to 10 July 2019, and provide a discussion forum for current active topics.

== Agenda ==

{| {{Tablestyle}}|-
! {{Headcellstyle}} | time
! {{Headcellstyle}} | activity
! {{Headcellstyle}} | title
|-
! 9:30 - 10:00
| align="center" style="background:#dce6f1" | plenary
| style="background:#dce6f1" | [[media:Introduction canSAS presentation-X.pdf‎ | Welcome and Introduction to canSAS]] - Paul Butler (NIST-CNR) and Adrian Rennie (Uppsala)
|-
! 10:00 - 10:45
| align="center" style="background:bisque" | discussion
| style="background:bisque"| Update/discussion on [[canSAS-IX]] activities - moderator: Grethe Jensen (University of Delaware/NIST-CNR)
|-
! 10:45 - 11:15
| align="center" style="background:#f2f2f2" | break
| style="background:#f2f2f2" | coffee
|-
! 11:15 - 11:30
| align="center" style="background:#e4dfec" | plenary
| style="background:#e4dfec" | [[media:canSAS_XI_presentation.pdf | July 2019 canSAS XI meeting update]] - Henrich Frielinghaus (Julich)
|-
! 11:30 - 12:00
| align="center" style="background:bisque" | discussion
| style="background:bisque" | NXcanSAS 2.0 discussion - Leader: Tim Snow (Diamond Light Source)
|-
! 12:00 - 13:30
| align="center" style="background:#f2f2f2" | lunch
| style="background:#f2f2f2" | ...
|-
! rowspan="4"| 13:30 - 14:20
| rowspan="4" align="center" style="background:bisque" | Discussion: Standards/Round Robins
| style="background:#dce6f1"| - ISO standards Development- Leader: Michael Krumrey (PTB)
|-
| style="background:#ffdc6d"| - Geosciences validation and round robin - Leader: Paul Butler(NIST-CNR) for Larry Anovitz (ORNL)
|-
| style="background:#f2dcdb"| - Other standards/round robin possiblities - Leader: Adrian Rennie (Uppsala Uni.)
|-
| style="background:#e4dfec"| -
|-
! 14:20 - 14:35
| align="center" style="background:bisque"| discussion
| style="background:bisque" | Education and Information: SAS video competition +... - moderator Pete Jemian (ANL)
|-
! 14:35 - 14:40
| align="center" style="background:#f2f2f2" | Group Photo
| style="background:#f2f2f2" | Outside if possible
|-
! 14:40 - 15:10
| align="center" style="background:#f2f2f2" | break
| style="background:#f2f2f2" | coffee
|-
! rowspan="4"| 15:10 - 15:50
| rowspan="4" align="center" style="background:bisque" | Discussion: Analysis Software collaborative Opportunities
| style="background:#dce6f1"| - Correlative Analysis and COST action - Leader: Brian Pauw (BAM)
|-
| style="background:#ffdc6d"| - Data and/or code repositories - Leader: Eliot Gann (NIST-NSLSII)
|-
| style="background:#f2dcdb"| - Other opportunities (machine learning/MD simulations etc) - Leader: Paul Butler(NIST-CNR)
|-
| style="background:#e4dfec"| -
|-
! 15:50 - 16:10
| align="center" style="background:bisque"| discussion
| style="background:bisque" | Open Mic: Other topics of interest to attendees - moderator Andrew Jackson (ESS)
|-
! 16:10 - 17:00
| align="center" style="background:bisque"| discussion
| style="background:bisque" | Discussion on topics and organization of [[canSAS-XI]] - moderator: Brian Pauw (BAM)
|-
! 17:00
| align="center" style="background:#f2f2f2" | ADJOURN
| style="background:#f2f2f2" | Adjourn to SAS2018 Opening Reception
|}

== Venue and Registration ==

* date: Sunday, October 7, 2018
* place: Peninsula Room C, Grand Traverse Resort & Spa, Traverse City, Michigan, USA
* (just before [https://sas2018.anl.gov/ SAS2018])

Note that as a "grass roots" community effort there are generally no specific funds to support the local organizing expenses of such meetings. Instead these expenses will be covered through mostly small registration fees asked of each participant. (Expect $30 to cover the two coffee breaks). Lunch is not included.

== Participants ==

[[File:canSAS-X participants.JPG | 400px ]]

== Meeting Topics ==

The topics being addressed at the canSAS X workshop are:

* Status of ongoing activities
* [[canSAS-XI | canSAS XI]] planning. Practical information at http://www.fz-juelich.de/jcns/EN/Leistungen/ConferencesAndWorkshops/canSASXI/_node.html
* NXcanSAS data formats and proposed improvements.
** improve the description of how Q should be provided in the HDF5 file
** Other needs?
* Planning new round-robin samples/measurements/data treatment
** Geosciences USAS: rocks/shales
** particle sizing standards?
** Other candidates?
* Collaborative opportunities for advancing data analysis tools
** COST action
** International "networking" or "collaboration grants
** Other
* disseminate information about canSAS and to recruit active participants to canSAS activities
* Other topics as might be of interest to those present - everyone is welcome to raise ideas as to what needs to be done and how to progress. There is a specific 'Open Mic' period in the timetable.

== Report on the Meeting ==

Everyone is encouraged to contribute to the meeting report and to post slides and other relevant material.

* The introduction to canSAS (P. Butler, A. Rennie) described briefly the activities and the success over the past 20 years since the first meeting in Grenoble, France. Particular aims for the day were reiterated with an emphasis that there are many on-going and new activities. Today there should be reports on status and plans for actions. A significant aim should be to prepare for the workshop next year in Freising, Germany (8-10 July 2019):
http://www.fz-juelich.de/jcns/EN/Leistungen/ConferencesAndWorkshops/canSASXI/_node.html

Introductory Slides. [[media:Introduction canSAS presentation-X.pdf‎ | Presentation]]

It was noted that some people were delayed in their arrival and others would have to mention relevant themes.

* The progress on tasks identified at canSAS-IX was reviewed. Grethe Jensen led this discussion.

* The location and arrangements for canSAS-XI were presented by Henrich Frielinghaus. [[media:canSAS_XI_presentation.pdf | Slides]]

=== 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.

Additionally discussion was had about:

* 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

* 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.

=== Correlative Analysis and COST Action ===

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.

Aside from the academic network, the proposal also had provision for a training and outreach network designed to engage the community and build a mass of users behind it for when the initial tranche of funding came to a close.

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.

=== Open Microphone Session ===

* An open question was posed - given the potential to develop/build an algorithm that could sift through, and/or analyse, user data in real-time:
** a) What would the canSAS group wish to get out of such an algorithm - how far ''should'' it go?
** b) How would it be possible to prevent it becoming a ''black-box''?
** c) How would one display to users of such an algorithm that there is, usually, no '''one''' correct answer and that you may have to subsequently look at, or cross-correlate, a given result?

== Local Organizing Committee ==

* SAS2018 organizers

== Program Committee ==

* Paul Butler (NIST, US)
* Adrian Rennie (Uppsala University, Sweden)
* Pete Jemian (APS, US)
* Henrich Frielinghaus (JCNS, Germany)

AnalysisGroupD

2017-06-14T15:38:05Z

Tim.snow:

NOTES FOR GROUP D

Tim Snow Leading

==Modelling 2D data==

* Everyone agreed that modelling 2D data has the potential to deliver more information than analysing 1D data, however, routinely analysing 2D data is not currently done
* Fitting of 2D data requires careful thought if down sampling is required as features could be missed, conversely fitting a Pilatus 2M image will take a long time

==Simulations and evolving algorithms==

* Projects coupling simulation with data fitting exist, although are typically in the earlier stages of development (i.e. SASSIE)
* The next generation of algorithms are anticipated to revolve around either optimised simulation fitting or machine learning
* Both approaches require a computing resource beyond a single desktop/laptop
* Collaborations with institution HPC or national HPC are likely required
* Additionally, links to commercial HPC/machine learning could be used for data fitting

==Automation==

* Automation of data acquisition requires care as many variables change dynamically
** Automatic alignment of some sample environments is challenging to human operators, let alone algorithms
** Deducing when 'good' data has been obtained is tricky, especially if the sample is liable to beam damage
** Determining an experimental endpoint could prove tricky too

* Automation of static scans is a good starting point
* Automatic data reduction should follow on from DAQ, however, fitting will likely require human intervention
* Automatic creation and archival of sample meta-data would prove highly useful for machine learning

==Collaborative funding strategies==

* Scientific funding is, as ever, extremely tight (however, also under increasingly close scrutiny as well...)
* Combining efforts and collaborating is likely to give governments / funding bodies good reason to fund projects as facilities / institutions can point towards shared (i.e. free(ish)) resources and get 'more bang for your buck'
* Finding common areas would be a positive step
** Data analysis
** Data fitting
** Identification of data quality
** Ways to automate different SAS measurements/techniques
** Code development
** Code maintenance/archiving
** Experimental meta-data
** Computing resource sharing (i.e. HPC)

* Events, such as canSAS, a good way to start such links
* Attending conferences either nationally or internationally a good way to form links with institutions, companies or funding bodies as well as other researchers

InfoGroupB

2017-06-06T00:28:25Z

Tim.snow:

==Education, information and outreach==

===What is lacking & what is feasible===

* An overview, a single resource providing a 'scattering 101' where users can go from no knowledge to some degree of competency

* Expectation handling, going from institution instruments, i.e. AFM, SEM, TEM, where results are visual and easily forthcoming to SAS

* Sample preparation best practices

* What's not possible!

===Creating new instructional material===

* No-one reads manuals!

* Videos (YouTube, etc.) are currently the favoured visual mechanism

* Simple phone/web apps that demonstrate/simulate simple x-ray patterns from simple scenarios, i.e. * [https://sites.google.com/site/squireslab/teaching-resources/fiber-diffraction-and-gi-saxs Miller planes and diffraction from cubic symmetry]

* Podcasts? Presence at student / general conferences

===Aggregating existing instructional materials===

* There's a whole treasure trove of resources from a variety of backgrounds/specialisations, i.e. * gisaxs.org or the NIST tutorials
* Perhaps on cansas.org we should aggregate these together
* Anticipating user requirements, perhaps a drill-down list would hone their literature/knowledge search, i.e.
Is your sample solid / liquid: [liquid]
Do you anticipate spheres or cylinders: [spheres]
What kind of size range do you anticipate for your samples: [100 nm]
Result: After acquiring data you should be looking into shape fitting using x, y, z piece of software using a sphere model, here's a list of resources to help: ...

===Generating scientific case studies===

* Pulling in previous point with drill-down list generate a number of common studies, i.e. 100 nm latex spheres, from 2D data to reduced data to result (almost, if not a complete, working example)
* Case studies incorporating multi-modal data analysis, using AFM/SEM/TEM results as inputs or constraints for fitting

===NXcanSAS dissemination===

* Users don't really care about the file format, as long as it works
* Make common software work with NXcanSAS
* If required, make software available to convert NXcanSAS to text

===Development and maintenance of sasportal===

* Should link to existing material
* New material, if not created elsewhere, should be hosted here
* Maintenance is difficult as people are reluctant to volunteer time...

=== Final thoughts===

* Users will likely have other information, use this to inform experimental, data reduction and analytical constraints to work in harmony with this data, not SAXS gives size x, SANS size y and AFM size z.
* Use our websites to link to existing resources, identify holes in knowledge and either outsource or create the material needed
* Move away from reliance on written word/formula and embrace videos and interactive applications
* Drop-down list to aid sample data acquisition/analysis routes

* An enforced, first time scattering users 'safety' video to aid understanding of what scattering experiments are capable of/can provide

InfoGroupB

2017-06-06T00:11:00Z

Tim.snow: