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Changes needed to support ONIX #360

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Changes needed to support ONIX #360

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30cf601
changes needed for onix
chrishalcrow Sep 1, 2025
8669835
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 1, 2025
37dbf9c
further onix fun
chrishalcrow Sep 28, 2025
ececc17
Clean up ONIX reader for openeohys and add tests
alejoe91 Oct 1, 2025
feaa386
Add NP2 onix data and support SELECTED_ELECTRODES
alejoe91 Oct 7, 2025
c52aee1
Only support SELECTED_ELECTRODES, not SELECTED_CHANNELS
alejoe91 Oct 7, 2025
35c5a2d
Add more NP2 onix test files
alejoe91 Oct 13, 2025
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59 changes: 40 additions & 19 deletions src/probeinterface/neuropixels_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -744,6 +744,7 @@ def read_openephys(
oe_version = parse(info_chain.find("VERSION").text)
neuropix_pxi_processor = None
onebox_processor = None
onix_processor = None
for signal_chain in root.findall("SIGNALCHAIN"):
for processor in signal_chain:
if "PROCESSOR" == processor.tag:
Expand All @@ -752,8 +753,10 @@ def read_openephys(
neuropix_pxi_processor = processor
if "OneBox" in name:
onebox_processor = processor
if "ONIX" in name:
onix_processor = processor

if neuropix_pxi_processor is None and onebox_processor is None:
if neuropix_pxi_processor is None and onebox_processor is None and onix_processor is None:
if raise_error:
raise Exception("Open Ephys can only be read when the Neuropix-PXI or the " "OneBox plugin is used.")
return None
Expand All @@ -769,6 +772,8 @@ def read_openephys(
if onebox_processor is not None:
assert neuropix_pxi_processor is None, "Only one processor should be present"
processor = onebox_processor
if onix_processor is not None:
processor = onix_processor

if "NodeId" in processor.attrib:
node_id = processor.attrib["NodeId"]
Expand Down Expand Up @@ -797,14 +802,20 @@ def read_openephys(
has_streams = False
probe_names_used = None

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The list of probe names for the test file are:

probe_names_used=['BreakoutBoard-DigitalIO', 'BreakoutBoard-AnalogIO-AnalogInput', 'BreakoutBoard-MemoryMonitor-PercentUsed', 'PortB-Neuropixels1.0eHeadstage-Probe', 'PortB-Neuropixels1.0eHeadstage-BNO055']

I think PortB-Neuropixels1.0eHeadstage-Probe is the one we're interested int? What are the others??

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That is correct, the PortB-Neuropixels1.0eHeadstage-Probe is the Neuropixels probe. The other streams are for other devices not related to Neuropixels. For reference, streams that start with BreakoutBoard are devices on the ONIX Breakout Board, and can be ignored for the purposes of SpikeInterface parsing. The BNO055 is a device on the Neuropixels headstage, and can also be ignored in this PR.

if onix_processor is not None:
probe_names_used = [probe_name for probe_name in probe_names_used if "Probe" in probe_name]

# for Open Ephys version < 1.0 np_probes is in the EDITOR field.
# for Open Ephys version >= 1.0 np_probes is in the CUSTOM_PARAMETERS field.
editor = processor.find("EDITOR")
if oe_version < parse("0.9.0"):
np_probes = editor.findall("NP_PROBE")
else:
custom_parameters = editor.find("CUSTOM_PARAMETERS")
np_probes = custom_parameters.findall("NP_PROBE")
if onix_processor is not None:
np_probes = custom_parameters.findall("NEUROPIXELSV1E")
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Will NEUROPIXELSV1E always be the name of the probe?

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I think it might be V1 or V2 depeneding on Neuropixels1.0/2.0. @bparks13 could you confirm?

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Currently the available options are NEUROPIXELSV1E, NEUROPIXELSV1F, and NEUROPIXELSV2E. The V1E/V1F are both Neuropixels 1.0 probes, and can be used interchangeably at this stage, the E/F distinction is differentiating the other ONIX hardware/headstage.

else:
np_probes = custom_parameters.findall("NP_PROBE")

if len(np_probes) == 0:
if raise_error:
Expand Down Expand Up @@ -839,13 +850,21 @@ def read_openephys(
# now load probe info from NP_PROBE fields
np_probes_info = []
for probe_idx, np_probe in enumerate(np_probes):
slot = np_probe.attrib["slot"]
port = np_probe.attrib["port"]
dock = np_probe.attrib["dock"]
probe_part_number = np_probe.attrib["probe_part_number"]
probe_serial_number = np_probe.attrib["probe_serial_number"]
# read channels
channels = np_probe.find("CHANNELS")
if onix_processor is not None:
slot, port, dock = None, None, None
probe_part_number, probe_serial_number = (
np_probe.attrib["probePartNumber"],
np_probe.attrib["probeSerialNumber"],
)
channels = np_probe.find("SELECTED_CHANNELS")
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Here, the names of several settings are slightly different than the other cases. e.g. ONIX uses probePartNumber instead of probe_part_number.
Also, I don't think ONIX stores the slot, port and dock? Or maybe PortB in the probe_names_used says which port is used?

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In terms of naming, some of these elements have been introduced in the draft PR here, which gives us some flexibility with changing the names. I could modify the name to be probe_part_number if that makes more sense to be consistent.

Since we are recording from Open Ephys hardware, and not IMEC hardware, we do not have a slot/port/dock to report. The Port in this instance is specifying which port on the Breakout Board the headstage is connected to.

else:
slot = np_probe.attrib["slot"]
port = np_probe.attrib["port"]
dock = np_probe.attrib["dock"]
probe_part_number = np_probe.attrib["probe_part_number"]
probe_serial_number = np_probe.attrib["probe_serial_number"]
channels = np_probe.find("CHANNELS")

channel_names = np.array(list(channels.attrib.keys()))
channel_ids = np.array([int(ch[2:]) for ch in channel_names])
channel_order = np.argsort(channel_ids)
Expand All @@ -862,18 +881,20 @@ def read_openephys(
else:
shank_ids = None

electrode_xpos = np_probe.find("ELECTRODE_XPOS")
electrode_ypos = np_probe.find("ELECTRODE_YPOS")
if onix_processor is None:
electrode_xpos = np_probe.find("ELECTRODE_XPOS")
electrode_ypos = np_probe.find("ELECTRODE_YPOS")

if electrode_xpos is None or electrode_ypos is None:
if raise_error:
raise Exception("ELECTRODE_XPOS or ELECTRODE_YPOS is not available in settings!")
return None
xpos = np.array([float(electrode_xpos.attrib[ch]) for ch in channel_names])
ypos = np.array([float(electrode_ypos.attrib[ch]) for ch in channel_names])
positions = np.array([xpos, ypos]).T
if electrode_xpos is None or electrode_ypos is None:
if raise_error:
raise Exception("ELECTRODE_XPOS or ELECTRODE_YPOS is not available in settings!")
return None
xpos = np.array([float(electrode_xpos.attrib[ch]) for ch in channel_names])
ypos = np.array([float(electrode_ypos.attrib[ch]) for ch in channel_names])
positions = np.array([xpos, ypos]).T
else:
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This seems like the hardest thing: electrode positions are not saved with ONIX, but they are for the other formats.

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yep, I think that the easiest would be to store the electrode x/y positions, or the selected electrods. In the latter case, we could instantiate a full NP probe from the probe part number and slice it accordingly.

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We are currently storing the selected electrodes in the settings.xml file, under the SELECTED_CHANNELS node. The indices are the global electrode index. I would be happy to talk through how it is currently set up, and we can determine if that information is enough or I can add in more details as needed.

positions = np.reshape(np.arange(0, 384 * 2 * 20, 20), shape=(384, 2))

probe_part_number = np_probe.get("probe_part_number", None)
pt_metadata, _, mux_info = get_probe_metadata_from_probe_features(probe_features, probe_part_number)

shank_pitch = pt_metadata["shank_pitch_um"]
Expand Down