Welcome to fpd’s documentation!

A python package for fast pixelated detector data storage, analysis and visualisation.

The fpd package provides code for the storage, analysis and visualisation of data from fast pixelated detectors. The data storage uses the hdf5 based EMD file format, and the conversion currently supports the Merlin readout from Medipix3 detectors. Differential phase contrast imaging and several other common data analyses, like radial distributions, virtual apertures, and lattice analysis, are also implemented, along with many utilities and general electron microscopy related tools.

The package is relatively lightweight, with most of its few dependencies being standard scientific libraries. All calculations run on CPUs and many use out-of-core processing, allowing data to be visualised and processed on anything from very modest to powerful hardware.

News

25 March 2021 - Release 0.2.0 with automatic threading control and several updates and improvements - see changelog for details.

23 January 2021 - Release 0.1.13 with several updates and improvements - see changelog for details.

21 December 2020 - Release 0.1.12 with several updates and improvements - see changelog for details.

1 November 2020 - Release 0.1.11 with lots of new features and improvements - see changelog for details.

4 September 2020 - Publication: Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post Acquisition Data Processing, Visualisation, and Structural Characterisation, Microsc. Microanal. 26, 944 (2020), arXiv (2019).

See News Archive for earlier news.

fpd-demos overview

Many examples of application of the fpd package are included in the fpd-demos repository: https://gitlab.com/fpdpy/fpd-demos

Citing

If you find this software useful and use it to produce results in a puplication, please consider citing the website or related paper(s).

An example bibtex entry with the date in the note field yet to be specified:

>>>
@Misc{fpd,
    Title                    = {{FPD: Fast pixelated detector data storage, analysis and visualisation}},
    howpublished             = {\url{https://gitlab.com/fpdpy/fpd}},
    note                     = {{Accessed} todays date}
}
>>>

Aspects of the library are covered in a paper:

https://zenodo.org/badge/DOI/10.5281/zenodo.3479124.svg https://zenodo.org/badge/DOI/10.5281/zenodo.3903517.svg

Publications

Some of the known scientific papers that used the fpd library are listed below. If you use the library for results contributing to a publication, please pass the paper details to developers for inclusion in this list.

  • Correlative chemical and structural nanocharacterization of a pseudo-binary 0.75Bi(Fe0.97Ti0.03)O3-0.25BaTiO3 ceramic,

J. Am. Ceram. Soc. 104, 2388 (2021), arXiv (2020).

  • Formations of narrow stripes and vortex-antivortex pairs in a quasi-two-dimensional ferromagnet K2CuF4,

J. Phys. Soc. Jpn. 90, 014702 (2021), Enlighten: Publications (2020).

  • Tunable superconductivity in Fe-pnictide heterointerfaces by diffusion control,

arXiv (2020).

  • Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part II: Post Acquisition Data Processing, Visualisation, and Structural Characterisation,

Microsc. Microanal. 26, 944 (2020), arXiv (2020).

  • Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing and Storage,

arXiv (2019), Microsc. Microanal. 26, 653 (2020).

  • Spontaneous creation and annihilation dynamics and strain-limited stability of magnetic skyrmions,

arXiv (2019), Nat. Commun. 11, 3536 (2020).

  • Tensile deformations of the magnetic chiral soliton lattice probed by Lorentz transmission electron microscopy,

arXiv (2019), Phys. Rev. B 101, 184424 (2020).

  • Sub-100 nanosecond temporally resolved imaging with the Medipix3 direct electron detector,

arXiv (2019), Ultramicroscopy, 210, 112917 (2020).

  • Strain Anisotropy and Magnetic Domains in Embedded Nanomagnets,

Small, 1904738 (2019).

  • Heisenberg pseudo-exchange and emergent anisotropies in field-driven pinwheel artificial spin ice,

arXiv (2019), Phys. Rev. B 100, 174410 (2019).

  • Order and disorder in the magnetization of the chiral crystal CrNb3S6,

arXiv (2019), Phys. Rev. B 99, 224429 (2019).

Indices and tables