Problem sorting NP1e data with kilosort

[RobertoDF]

Hi,

I just sorted my first ONIX rec using kilosort. This animal has been recorded lin the past using another system and showed a good number of units. However it looks like this after sorting on the ONIX:
https://github.com/user-attachments/assets/63af81d6-f5ed-46ae-907c-4f8b9013195e

Weirdly many units seems upside down. The problem is not resolved if I invert the traces though!

I used this script here:

import os
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
import spikeinterface.extractors as se
import spikeinterface.widgets as sw
import probeinterface
import probeinterface.plotting
from pathlib import Path
from probeinterface import  read_probeinterface

ap_gain = 1000 
lfp_gain = 50 
bit_depth = 10
suffix = 6 # Change to match file names' suffix
sampling_frequency = 3e4
num_channels = 384 # Decrease channels to expedite plotting and inspect fewer traces

path_recording_folder = Path(r"X:\data\74\20250128")

probeinterface_filename = 'np1-config.json'

probes = read_probeinterface(Path(path_recording_folder, probeinterface_filename))

ap_scalar = 1.2e6 / (2 ** bit_depth) / ap_gain
ap_offset = (2 ** (bit_depth - 1)) * ap_scalar
ap_recording = se.read_binary(os.path.join(path_recording_folder,  f"np1-spike_{suffix}.raw"), 
                         sampling_frequency, 
                         np.uint16, 
                         num_channels, 
                         gain_to_uV=ap_scalar, 
                         offset_to_uV=-ap_offset) 

ap_recording = ap_recording.set_probegroup(probe)

binary_file_path = os.path.join(path_recording_folder,  f"np1-spike_{suffix}.raw")

probe_filename = f"{path_recording_folder}/spike_interface_output/probe{probe_n}/sorter_output/probe.prb"

pg =  ap_recording.get_probegroup()
write_prb(probe_filename, pg)
print(f"probe {probe_n} completed \n")

probe = load_probe(probe_filename)
settings = {'filename': binary_file_path,
            "n_chan_bin": probe["n_chan"], "fs": ap_recording.get_sampling_frequency()}

result_dir = path_recording_folder / "spike_interface_output" / f"probe0" / "sorter_output"
os.makedirs(result_dir, exist_ok=True)

run_kilosort(settings=settings, probe=probe, data_dtype=sub_rec.get_dtype(),
             device=torch.device("cuda"), results_dir=result_dir, clear_cache=True)

[RobertoDF]

Just realized the binary file I am feeding kilosort is not scaled! I ll try again