locan.locan_io.locdata

File input/output for localization data.

There are functions for reading the following file structures (with an indicator string in parenthesis - see also locan.constants.FileType):

• custom text file (CUSTOM)

• rapidSTORM file format (RAPIDSTORM) [1]

• Elyra file format (ELYRA)

• Thunderstorm file format (THUNDERSTORM) [2]

• asdf file format (ASDF) [3]

• Nanoimager file format (NANOIMAGER)

• rapidSTORM track file format (RAPIDSTORMTRACK) [1]

• smlm file format (SMLM) [4], [5]

• decode file (DECODE) [6]

• smap file format (SMAP) [7]

References

[1] (1,2)

Wolter S, Löschberger A, Holm T, Aufmkolk S, Dabauvalle MC, van de Linde S, Sauer M., rapidSTORM: accurate, fast open-source software for localization microscopy. Nat Methods 9(11):1040-1, 2012, doi: 10.1038/nmeth.2224

[2]

M. Ovesný, P. Křížek, J. Borkovec, Z. Švindrych, G. M. Hagen. ThunderSTORM: a comprehensive ImageJ plugin for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 30(16):2389-2390, 2014.

[3]

Greenfield, P., Droettboom, M., & Bray, E., ASDF: A new data format for astronomy. Astronomy and Computing, 12: 240-251, 2015, doi:10.1016/j.ascom.2015.06.004

[4]

Ouyang et al., Deep learning massively accelerates super-resolution localization microscopy. Nat. Biotechnol. 2018, doi:10.1038/nbt.4106.

[5]

https://github.com/imodpasteur/smlm-file-format

[6]

Artur Speiser, Lucas-Raphael Müller, Philipp Hoess, Ulf Matti, Christopher J. Obara, Wesley R. Legant, Anna Kreshuk, Jakob H. Macke, Jonas Ries, and Srinivas C. Turaga, Deep learning enables fast and dense single-molecule localization with high accuracy. Nat Methods 18: 1082–1090, 2021, doi:10.1038/s41592-021-01236-x

[7]

Ries, J., SMAP: a modular super-resolution microscopy analysis platform for SMLM data. Nat Methods 17: 870–872, 2020, doi.org/10.1038/s41592-020-0938-1

Submodules:

io_locdata	File input/output for localization data.
utilities	Utility functions for file input/output of localization data.
rapidstorm_io	File input/output for localization data in rapidSTORM files.
thunderstorm_io	File input/output for localization data in Thunderstorm files.
elyra_io	File input/output for localization data in Elyra files.
nanoimager_io	File input/output for localization data Nanoimager files.
asdf_io	File input/output for localization data in ASDF files
smlm_io	File input/output for localization data in SMLM files.
decode_io	File input/output for localization data in DECODE files.
smap_io	File input/output for localization data in SMAP files.