https://github.com/whitews/flowio

A Python library for reading and writing Flow Cytometry Standard (FCS) files
https://github.com/whitews/flowio

cytometry fcs fcs-files flow-cytometry flow-cytometry-analysis flow-cytometry-files immunology python

Last synced: about 2 months ago
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A Python library for reading and writing Flow Cytometry Standard (FCS) files

• Host: GitHub
• URL: https://github.com/whitews/flowio
• Owner: whitews
• License: bsd-3-clause
• Created: 2013-11-23T02:03:08.000Z (over 11 years ago)
• Default Branch: master
• Last Pushed: 2025-03-28T22:06:55.000Z (2 months ago)
• Last Synced: 2025-03-30T00:05:00.108Z (2 months ago)
• Topics: cytometry, fcs, fcs-files, flow-cytometry, flow-cytometry-analysis, flow-cytometry-files, immunology, python
• Language: Python
• Homepage: https://flowio.readthedocs.io
• Size: 11.5 MB
• Stars: 45
• Watchers: 4
• Forks: 22
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# FlowIO

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## Overview

FlowIO is a Python library for reading / writing Flow Cytometry Standard (FCS) 

files, with zero external dependencies and is compatible with Python 3.7+.

FlowIO retrieves event data exactly as it is encoded in the FCS file: as a 

1-dimensional list without separating the events into channels or performing 

any preprocessing (e.g. applying gain). Metadata stored in the FCS file is 

available as a dictionary via the 'text' attribute. Basic attributes are also 

available for commonly accessed properties. For example, the channel count 

can be used to easily convert the event data to a multi-column NumPy array:

```

import flowio

import numpy

fcs_data = flowio.FlowData('example.fcs')

npy_data = numpy.reshape(fcs_data.events, (-1, fcs_data.channel_count))

```

For higher level interaction with flow cytometry data, including GatingML and FlowJo 10 support, 

see the related [FlowKit](https://github.com/whitews/FlowKit) project.

## Installation

The recommended way to install FlowIO is via the `pip` command:

```

pip install flowio

```

Or, if you prefer, you can install from the GitHub source:

```

git clone https://github.com/whitews/flowio

cd flowio

pip install .

```

## Documentation

The FlowIO API documentation is available [on ReadTheDocs here](https://flowio.readthedocs.io/en/latest/?badge=latest). If you have any questions about FlowIO or find any bugs [please submit an issue to the GitHub repository here](https://github.com/whitews/FlowIO/issues/new/).

### Changelogs

[Changelogs for versions are available here](https://github.com/whitews/FlowIO/releases)