Read Becker & Hickl SDT files


Keywords
fluorescence-lifetime-spectroscopy, fluorescence-microscopy-imaging, format-reader, photon-counting, python
License
BSD-3-Clause
Install
pip install sdtfile==2019.1.1

Documentation

Read Becker & Hickl SDT files

Sdtfile is a Python library to read SDT files produced by Becker & Hickl SPCM software. SDT files contain time correlated single photon counting instrumentation parameters and measurement data. Currently only the "Setup & Data", "DLL Data", and "FCS Data" formats are supported.

Becker & Hickl GmbH is a manufacturer of equipment for photon counting.

Author: Christoph Gohlke
License: BSD 3-Clause
Version: 2023.8.30

Quickstart

Install the sdtfile package and all dependencies from the Python Package Index:

python -m pip install -U sdtfile

See Examples for using the programming interface.

Source code and support are available on GitHub.

Requirements

This revision was tested with the following requirements and dependencies (other versions may work):

Revisions

2023.8.30

  • Fix linting issues.
  • Add py.typed marker.
  • Drop support for Python 3.8 and numpy < 1.22 (NEP29).

2022.9.28

  • Convert docstrings to Google style with Sphinx directives.

2022.2.2

  • Add type hints.
  • Drop support for Python 3.7 and numpy < 1.19 (NEP29).

2021.11.18

  • Fix reading FLIM files created by Prairie View software (#5).

2021.3.21

  • Add sdt2dat script.

2020.12.10

  • Fix shape of non-square frames.

2020.8.3

  • Fix integer overflow (#3).
  • Support os.PathLike file names.

2020.1.1

  • Fix reading MCS_BLOCK data.
  • Remove support for Python 2.7 and 3.5.
  • Update copyright.

2019.7.28

  • Fix reading compressed, multi-channel data.

2018.9.22

  • Use str, not bytes for ASCII data.

2018.8.29

  • Move module into sdtfile package.

2018.2.7

  • Bug fixes.

2016.3.30

  • Support revision 15 files and compression.

2015.1.29

  • Read SPC DLL data files.

2014.9.5

  • Fix reading multiple MEASURE_INFO records.

References

  1. W Becker. The bh TCSPC Handbook. Third Edition. Becker & Hickl GmbH 2008. pp 401.
  2. SPC_data_file_structure.h header file. Part of the Becker & Hickl SPCM software.

Examples

Read image and metadata from a "SPC Setup & Data File":

>>> sdt = SdtFile('image.sdt')
>>> sdt.header.revision
588
>>> sdt.info.id[1:-1]
'SPC Setup & Data File'
>>> int(sdt.measure_info[0].scan_x[0])
128
>>> len(sdt.data)
1
>>> sdt.data[0].shape
(128, 128, 256)
>>> sdt.times[0].shape
(256,)

Read data and metadata from a "SPC Setup & Data File" with multiple data sets:

>>> sdt = SdtFile('fluorescein.sdt')
>>> len(sdt.data)
4
>>> sdt.data[3].shape
(1, 1024)
>>> sdt.times[3].shape
(1024,)

Read image data from a "SPC FCS Data File" as numpy array:

>>> sdt = SdtFile('fcs.sdt')
>>> sdt.info.id[1:-1]
'SPC FCS Data File'
>>> len(sdt.data)
1
>>> sdt.data[0].shape
(512, 512, 256)
>>> sdt.times[0].shape
(256,)