The philosophy behind the Open Ephys GUI differs from that of existing commercial software for neuroscience. Taking inspiration from audio processing software such as Ableton Live, the GUI is structured around independent modules that can be mixed and matched to build a custom signal chain. We hope that this structure will give users and developers a tremendous amount of flexibility, without compromising functionality.
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Because of how the GUI is structured, recording has to work a little differently than it does in traditional electrophysiology applications. It makes few assumptions about what data you actually want to save. The default is to record only events, not continuous channelsBy default, the GUI records only continuous data from "Source" processors. To record continuous data at other points in the processing pipeline, you have to manually select the channels you'd like to save from within an individual module. If you really want to, you can save every channel at every step in the signal chain. Or, you can choose to dump all save the raw data to disk, while ignoring the rest of the pipeline. Or, you can save the data only after it's been data only after it's been filtered and processed in specific ways. As you can see, this approach gives the user tremendous flexibility, but can also lead to confusion when you first use the software. We are obviously open to suggestions for ways to make the recording process more transparent and intuitive.
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The data files won't be saved directly in this directory, but rather inside another directory that will be created inside this folder. Unlike in Neuralynx software, this This sub-folder won't be created _unless you actually record data_.
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All events that flow through the signal chain are saved automatically into a file called `all_channels.events` (or experimentX.kwe, if you're using the Kwik data format). This includes both events that are generated by external devices (such as TTLs) and events that are emitted by modules within the application. There's currently no way to disable saving events.
This is a long-winded way of saying you don't have to do anything special to save events; they will be recorded by default.
Recording continuous data
Selecting continuous channels for recording is done through an interface within
Recording continuous data
Selecting continuous channels for recording is done through an interface within each module.
- Click the vertical bars on the right side of the File Reader to open the channel selector drawer.
- Click the "REC" button to see the channels that can be saved within this module.Click the "ALL"
- button to select all the channels. If you left it like this, it would save all 16 channels after All of the channels should be selected by default, meaning data from all 16 channels will be saved as soon as the record button is pressed.
- Click the "NONE" button to deselect all the channels. This restores the default state, in which no continuous channels are In this state, none of the data from this module will be saved.
- Click on the numbers 1, 2, and 3 to select the first three channels for savingto select the first three channels for saving. Now, only channels 1-3 will be saved. The recording state is summarized in the Graph tab.
- Click the vertical bars again to close the drawer.
Now we've configured the GUI to save the first three channels of data that come into the File Reader. If you want to save data from other modules, such as after it's been bandpass filtered, go through the steps above and select the appropriate channels.
Data In the Open Ephys data format, data from each channel is saved in its own file, with the title "XXX_YYY.continuous", where XXX = the ID number of the module it came from and YYY = the channel number within that module. To translate the module ID back to its name, you can look at the XML settings file that is saved along with the recorded data.
In the Kwik format, all the data from an individual processor is saved in the same HDF5 file.
For more information on how the data is stored, check out the [[data format]] page on the wiki.
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Once the files are saved, it's easy to load the data into Matlab or Python. We've created the a load_open_ephys_data m-file an OpenEphys.py file that requires require only the filename as input.
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The signal chain should be re-loaded exactly as you left it, including the parameters within each module. If it appears that something is changed, it could mean there's a bug in the loading code. In that case, consider submitting an issue if one doesn't already exist.
We have prepared some example configuration files that show some of the basic features described here. You can find them in Resources/Configs/ , or on github.
Alternatively, you can select the "Reload on startup" option from the "File" menu, which will automatically reload the last-used configuration the next time the application is launched.
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