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Read fluorescence correlation spectroscopy (FCS) data files

Project description

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:2020.1.1

Requirements

Revisions

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()

Project details


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