channel map information in the settings.xml

[alirezasaeedi1988]

The settings.xml file does not contain the channel map information (<ELECTRODE_XPOS ...> and <ELECTRODE_YPOS ...>).
It would be great to have that information saved in the setting.xml file (similar to neuropix-pxi) so that tools like SpikeInterface can load the probe information at once, together with the recording data.

settings.zip

[bparks13]

@alirezasaeedi1988 The channel map information is currently available in the ProbeInterface JSON file, if that’s helpful. To extract it, you can filter for device_channel_indices that are not equal to -1, and then use those indices to access the corresponding contact_positions, which provide the [x, y] coordinates of each electrode center.

When designing the current system, we chose not to include electrode positions in the XML file, mainly to simplify things when working with multiple configurations. At the time, it seemed more manageable to maintain separate JSON files rather than multiple XML files that differ only in electrode positions.

That said, we really appreciate your suggestion and will definitely keep it in mind as we continue to improve the format. Thank you for the feedback!

[bparks13]

Further clarification; when the OE GUI saves a recording, there is a settings.xml file that is also recorded within this directory, which is a copy of the signal chain that was used to record that particular set of data. Therefore, adding the electrode X/Y positions into the XML file will also be saved within this, allowing for functions from SpikeInterface (e.g., si.read_openephys) to open and read these XML files with the relevant data.

[bparks13]

After looking more into the format that the Neuropixels-PXI plugin uses, as well as the Spike Interface method to read the XML data, simply adding the channel map information will not allow automatic extraction of the probe group information. The function si.read_openephys calls probeinterface.read_openephys to extract the probe group information, but it then checks whether or not the source node is either PXI or OneBox, meaning that until we can get the underlying methods to be updated to allow ONIX Source as a valid source, nothing we change here will have an effect. We can still discuss what the next steps should be, and plan on which features / variables to add in the XML file, but this might not be a quick fix.

One option we do have in the meantime is to save a full ProbeInterface configuration JSON file manually, and then the processing steps can include:

import spikeinterface.full as si
import probeinterface as pi
from pathlib import Path

directory = Path('/path/to/directory')
raw_rec = si.read_openephys(directory, stream_id='1')

probe_file = Path('/path/to/probe_interface.json')
probegroup = pi.read_probeinterface(probe_file)

raw_rec.set_probegroup(probegroup, in_place=True)