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By automatically recording as much information as possible in automated laboratory setups, reproducibility and traceability of experiments are vastly improved. This presentation shows what such an approach means for the quality of experiments in an X-ray scattering laboratory and an automated synthesis set-up.
This presentation highlights ongoing scientific misconduct as found in academic literature. This includes data- and image manipulation, and paper mills. Starting with an expose of examples, it delves deeper into the causes and metrics driving this phenomenon. Finally a range of possible tools is presented, that the young researcher can use to prevent themselves from sliding into the dark scientific methods.
Trinamic TMCL IOC is a Python package designed for controlling stepper motors connected to a Trinamic board using the TMCL language (all boards supported by PyTrinamic should now work, has been tested on the TMCM 6110 and the TMCM 6214). Since it is implementing the TMCL protocol, it should be easy to adapt to other Trinamic motor controller boards. This package assumes the motor controller is connected over a machine network via a network-to-serial converter, but the underlying PyTrinamic package allows for other connections too.
This allows the control of attached motors via the EPICS Channel-Access virtual communications bus. If EPICS is not desired, plain Pythonic control via motion_control should also be possible. An example for this will be provided in the example.ipynb Jupyter notebook.
This package leverages Caproto for EPICS IOCs and a modified PyTrinamic library for the motor board control, and interfaces between the two via an internal set of dataclasses. Configuration for the motors and boards are loaded from YAML files (see tests/testdata/example_config.yaml).
The modifications to PyTrinamic involved extending their library with a socket interface. This was a minor modification that should eventually find its way into the official package (a pull request has been submitted).
This is a set of use examples for the HDF5Translator framework. This framework lets you translate measurement files into a different (e.g. NeXus-compatible) structure, with some optional checks and conversions on the way. For an in-depth look at what it does, there is a blog post here.
The use examples provided herein are each accompanied by the measurement data necessary to test and replicate the conversion. The README.md files in each example show the steps necessary to do the conversion for each.
We encourage those who have used or adapted one or more of these exampes to create their own conversion, to get in touch with us so we may add your example to the set.
Simulates X-ray and Neutron scattering patterns from arbitrary shapes defined by STL files.
Features:
- Uses multithreading to compute a number of independent solutions, then uses the variance of the results to estimate an uncertainty on the output.
- Can be launched from the command line using an excel sheet to define settings, or from a jupyter notebook.
- Outputs scattering patterns in absolute units if the contrast is set.
- A Gaussian size distribution is available, where the relative scaling of objects for each repetion can be varied. Recommended to be used with limited width (max. 10%) to avoid artefacts.
- Writes results with settings to an archival HDF5 file.
Application examples:
This software has been used in several studies to date. For example, it has been used here to simulate a model scattering pattern for a cuboid shape, which was then fed forward into the McSAS3 analysis program for analyzing scattering patterns of polydisperse cuboids. A second use is here, where it was used for the modeling of flattened helices. In this paper, scattering pattern features could be matched with particular morphological changes in the structure. Lastly, this paper has an example where it was used to validate the analytical analysis model, and explore the realistic limits of application of the analytical model.
OpenSCAD, STL and technical drawings for the capillary flow-through cell designed primarily for use with The MOUSE instruments.
This flow-through cell can be used in conjunction with:
- Modular sample holder (10.5281/zenodo.7499416)
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Laser-cut sample holder (10.5281/zenodo.7499437)
Technical drawings and documents for building a compact, heated, vacuum compatible flow-through sample holder. This holder is in use at the BAM MOUSE instrument as well as at the I22 beamline at the Diamond Light Source (see references for instrument details).
This holder has several features:
- The holder can be used in vacuum environments as well as in atmosphere
- It has two G 1/4" UNF fittings to attach HPLC tubing for (optionally) flowing a medium through the sample cell
- There are two additional (unflowed) sample positions for backgrounds and calibrants, held at the same temperature
- The low-mass design coupled with a 250W heating element can achieve heating rates of 1 degree C per second, when coupled (for example) with an Omron E5CC PID controller.
- The sample holder insert can be made from various materials depending on the application. Sealing the sample from the vacuum can be achieved using kapton, teflon or Magic tape, depending on the temperature requirements. The inlet and outlet holes will need to be punctured with a needle to enable flow.
- Large exit cones ensure a clear exit angle of at least 45 degrees two theta.
- It has been tested with temperatures up to 400 degrees C.
- Compression area has been raised and polished to ensure a good vacuum seal.
OpenSCAD, STL and technical drawings for the solid sample rack designed primarily for use with The MOUSE instruments.
This solid sample rack can be used in conjunction with:
- Laser-cut sample holder (10.5281/zenodo.7499437)
- Modular sample holder (10.5281/zenodo.7499416)
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)
PDF file for the laser-cut sample holder designed primarily for use with The MOUSE instruments.
This sample holder can be used in conjunction with:
- Solid sample rack/plate (10.5281/zenodo.7499424)
- Modular sample holder (10.5281/zenodo.7499416)
- Capillary flow-cell for liquid samples (10.5281/zenodo.7499421)