https://github.com/cgohlke/fcsfiles

Read fluorescence correlation spectroscopy (FCS) data files
https://github.com/cgohlke/fcsfiles

fluorescence-correlation format-reader python zeiss

Last synced: 2 months ago
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Read fluorescence correlation spectroscopy (FCS) data files

• Host: GitHub
• URL: https://github.com/cgohlke/fcsfiles
• Owner: cgohlke
• License: bsd-3-clause
• Created: 2020-02-22T22:40:03.000Z (almost 5 years ago)
• Default Branch: master
• Last Pushed: 2024-05-25T16:39:28.000Z (8 months ago)
• Last Synced: 2024-06-11T18:32:59.195Z (7 months ago)
• Topics: fluorescence-correlation, format-reader, python, zeiss
• Language: Python
• Homepage: https://pypi.org/project/fcsfiles
• Size: 38.1 KB
• Stars: 1
• Watchers: 2
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

        
..

  This file is generated by setup.py

Read fluorescence correlation spectroscopy (FCS) data files

===========================================================

Fcsfiles is a Python library to read Carl Zeiss(r) ConfoCor(r) RAW and ASCII

measurement data files.

:Author: `Christoph Gohlke `_

:License: BSD 3-Clause

:Version: 2024.5.24

Quickstart

----------

Install the fcsfiles package and all dependencies from the

`Python Package Index `_::

    python -m pip install -U fcsfiles

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):

- `CPython `_ 3.9.13, 3.10.11, 3.11.9, 3.12.3

- `NumPy `_ 1.26.4

Revisions

---------

2024.5.24

- Support NumPy 2.

- Fix docstring examples not correctly rendered on GitHub.

2023.8.30

- Fix linting issues.

- Add py.typed marker.

- Convert to Google style docstrings.

- Drop support for Python 3.8 and numpy < 1.22 (NEP29).

2022.9.28

- Update metadata.

2022.2.2

- Add type hints.

- Use float64 or int64 for ConfoCor3Fcs arrays.

- Drop support for Python 3.7 and numpy < 1.19 (NEP29).

2021.6.6

- Remove support for Python 3.6 (NEP 29).

2020.9.18

- Relax ConfoCor3Raw header requirement.

- Support os.PathLike file names.

2020.1.1

- Remove support for Python 2.7 and 3.5.

Notes

-----

"Carl Zeiss" and "ConfoCor" are registered trademarks of Carl Zeiss, Inc.

The use of this implementation may be subject to patent or license

restrictions.

The API is not stable yet and is expected to change between revisions.

This module does *not* read flow cytometry standard FCS files.

Examples

--------

Read the CountRateArray from a ConfoCor3 ASCII file as a numpy array:

.. code-block:: python

    >>> fcs = ConfoCor3Fcs('ConfoCor3.fcs')

    >>> fcs['FcsData']['FcsEntry'][0]['FcsDataSet']['CountRateArray'].shape

    (60000, 2)

    >>> print(fcs)  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE

    Carl Zeiss ConfoCor3 - measurement data file - version 3.0 ANSI

    BEGIN FcsData 30000

            Name = Fluorescein

            Comment =

            AverageFlags = Repeat|Position|Average_Fit_Results

            SortOrder = Channel-Repeat-Position-Kinetics

            BEGIN FcsEntry1 10000

    ...

Read data and metadata from a ConfoCor3 RAW file:

.. code-block:: python

    >>> fcs = ConfoCor3Raw('ConfoCor3.raw')

    >>> fcs.filename

    'f5ee4f36488fca2f89cb6b8626111006_R1_P1_K1_Ch1.raw'

    >>> fcs.frequency

    20000000

    >>> times = fcs.asarray()

    >>> times[10858]

    1199925494

    >>> times, bincounts = fcs.asarray(bins=1000)

    >>> times.shape

    (1000,)

    >>> bincounts[618]

    23

    >>> fcs.close()

Read data and metadata from a ConfoCor2 RAW file:

.. code-block:: python

    >>> fcs = ConfoCor2Raw('ConfoCor2.raw')

    >>> fcs.frequency

    20000000

    >>> ch0, ch1 = fcs.asarray()

    >>> ch1[4812432]

    999999833

    >>> times, ch0, ch1 = fcs.asarray(bins=1000)

    >>> times.shape

    (1000,)

    >>> ch1[428]

    10095

    >>> fcs.close()