File Reader

Annotated File Reader settings interface
Reads data from a local file.

Plugin Type

Source

Platforms

Windows, Linux, macOS

Built in?

Yes

Key Developers

Aarón Cuevas López, Pavel Kulik

Source Code

https://github.com/open-ephys/plugin-GUI/tree/main/Source/Processors/FileReader

Loading Data

By default, the File Reader is compatible with files saved in the Binary Format (indexed with a structure.oebin file). If the appropriate plugins are installed, the File Reader can also read data stored in the Open Ephys Format (indexed with a structure.openephys file) and NWB Format (saved inside a *.nwb file).

Note

Data saved by previous versions of the GUI may not load in version 0.6.x. For help updating your files to work with the latest File Reader, send a message to support@open-ephys.org.

Each input file can contain multiple streams/recordings, but only one stream/recording can be played back per File Reader during acquisition. The drop-down menu below the active file name makes it possible to switch between the available streams when acquisition is paused. In order to play multiple streams simultaneously, you can merge multiple File Readers, each with the same input file and a different selected stream.

You can play back a subset of a recorded file by changing the “start” and “end” times at the bottom of the File Reader editor.

File Scrubbing

For recordings longer than 30 seconds, a drawer button will appear on the left side of the File Reader to access the Scrubbing Interface. This interface makes it possible to quickly browse to different parts of the data file.

Full Timeline

The bottom timeline spans the length of the recording. The colored vertical bars along the timeline correspond to recorded events associated with the active stream. A slider along this timeline is fixed at a 30 second interval and allows adjusting the start and stop time for playback.

Zoom (30 Second) Timeline

The top timeline spans the currently selected interval of 30 seconds by the Full Timeline. The Zoom Timeline also contains a slider, however this slider can span anywhere from 1 to 30 seconds. The default value is 10 seconds. Moving the right slider handle adjusts the length of the selected interval. Moving the left slider handle moves the entire interval back and forth along the timeline. Clicking and dragging anywhere inside the interval also moves the entire interval along the timeline. Playback will automatically stop when it reaches the end of the current interval.

Playback Button

The playback button’s state indicates whether or not to playback the currently selected interval while acquisition is active. If the ‘pause state’ is showing, this means playback will be active during acquisition. If the ‘play state’ is showing, then playback will NOT be active during acquisition. Toggle the button to change to the desired state as needed.

Sample Data

By default, the File Reader reads a recording of 16 channels from 8 stereotrodes implanted in the barrel cortex of an awake mouse.

There are also four example files included in the GUI’s GitHub repository that can be used with the File Reader, found in the Resources/DataFiles directory.

  • data_stream_16ch_cortex - Same as the default data file. The signals contain many action potentials, and are useful for testing spike detection pipelines.

  • data_stream_16ch_hippocampus - One channel of data recorded from mouse CA1, replicated across 16 channels. The signals have large-amplitude theta oscillations, and can be used to test phase-triggered stimulation.

  • data_stream_sine_wave - 16 channels of a 1000-microvolt sine wave.

  • chirps_16_channels_At40kHz - 16 channels of frequency sweeps at 40 kHz.

Other input data

The File Reader should be able to read any datasets that have been previously saved by the GUI (v0.6.0+). If you make a recording that is not compatible with the File Reader for some reason, please send a message to support@open-ephys.org.