fcsfiles 2020.9.18

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

Organization:

Laboratory for Fluorescence Dynamics. University of California, Irvine

License:

BSD 3-Clause

Version:

2020.9.18

Requirements

• CPython >= 3.6

• Numpy 1.15.1

Revisions

2020.9.18

Relax ConfoCor3Raw header requirement.

2020.1.1

Remove support for Python 2.7 and 3.5. Update copyright.

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:

>>> fcs = ConfoCor3Fcs('ConfoCor3.fcs')
>>> fcs['FcsData']['FcsEntry'][0]['FcsDataSet']['CountRateArray'].shape
(60000, 2)

Read data and metadata from a ConfoCor3 RAW file:

>>> 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:

>>> 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()