spikeinterface: Probe missing when using run_sorter()

Hi, I hope this is just a user error on my part. I am trying to spike sort some data, the sorters appear to be working. However, even though a probe appears to be attached to the recording, run_sorter() says there is none. I have this issue for other sorters that require a probe map as well (spykingcircuis, kilosort, etc.), but not for mountainsort5 (I’m assuming due to some inherent difference in computation in MS5 not needing the probe).

import matplotlib.pyplot as plt
from pprint import pprint
import spikeinterface.full as si
from pathlib import Path
from probeinterface import get_probe
from probeinterface.plotting import plot_probe
import numpy as np

camb_64x1 = get_probe('cambridgeneurotech','ASSY-77-H3') #64x1 probe catalog number
camb64x1_tdt_map = np.array([12, 11, 4, 8, 16, 64, 1, 2, 13, 9, 10, 14, 6, 7, 5, 3, 50, 49, 52, 
                             51, 54, 53, 56, 55, 15, 63, 62, 61, 59, 60, 57, 58, 23, 28, 21, 22, 20, 
                             19, 18, 17, 42, 24, 29, 25, 30, 26, 31, 27, 46, 45, 40, 34, 37, 32, 33, 
                             41, 44, 47, 48, 43, 35, 38, 39, 36])
camb64x1_tdt_map = camb64x1_tdt_map - 1 # subtract for python indexing
camb_64x1.set_device_channel_indices(camb64x1_tdt_map)



base_folder = Path('E:/PFC_DREADDS/Record-230306-100339/r392_pfc_spon_bl1/') # so we can save binary files and such to the same data folder
tdt_tank = base_folder / 'Record-230306-100339_r392_pfc_spon_bl1.Tbk'
raw_data = si.read_tdt(tdt_tank,stream_name="b'SPKw'")


raw_data = raw_data.set_probe(camb_64x1)
probe_df = raw_data.get_probe().to_dataframe()
print(probe_df)

The output confirming the probe:

c:\Users\admin\anaconda3\envs\si_env\lib\site-packages\neo\rawio\tdtrawio.py:293: UserWarning: Could not identify sev files for channels [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]. warnings.warn(f"Could not identify sev files for channels {missing_sev_channels}.") x y contact_shapes width height shank_ids contact_ids 0 0.0 880.0 rect 11.0 15.0 7 1 0.0 700.0 rect 11.0 15.0 8 2 0.0 1160.0 rect 11.0 15.0 16 3 0.0 920.0 rect 11.0 15.0 3 4 0.0 800.0 rect 11.0 15.0 15 … … … … … … … … 59 0.0 1200.0 rect 11.0 15.0 30 60 0.0 980.0 rect 11.0 15.0 28 61 0.0 1100.0 rect 11.0 15.0 27 62 0.0 1020.0 rect 11.0 15.0 26 63 0.0 680.0 rect 11.0 15.0 6

[64 rows x 7 columns]

Probe not showing up for sorting

sorting = si.run_sorter(recording=raw_data, sorter_name='tridesclous2', output_folder= base_folder / 'tdc_map_test')

Output:

c:\Users\admin\anaconda3\envs\si_env\lib\site-packages\neo\rawio\tdtrawio.py:293: UserWarning: Could not identify sev files for channels [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]. warnings.warn(f"Could not identify sev files for channels {missing_sev_channels}.“) c:\Users\admin\anaconda3\envs\si_env\lib\site-packages\spikeinterface\core\baserecordingsnippets.py:244: UserWarning: There is no Probe attached to this recording. Creating a dummy one with contact positions warn(“There is no Probe attached to this recording. Creating a dummy one with contact positions”) c:\Users\admin\anaconda3\envs\si_env\lib\site-packages\neo\rawio\tdtrawio.py:293: UserWarning: Could not identify sev files for channels [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]. warnings.warn(f"Could not identify sev files for channels {missing_sev_channels}.”)

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Thank you very much for your help and this interface, Walker