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1 | 1 | """
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2 |
| -The following DataJoint pipeline implements the sequence of steps in the spike-sorting routine featured in the |
3 |
| -"spikeinterface" pipeline. |
4 |
| -Spikeinterface developed by Alessio Buccino, Samuel Garcia, Cole Hurwitz, Jeremy Magland, and Matthias Hennig (https://github.com/SpikeInterface) |
5 |
| -
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6 |
| -The DataJoint pipeline currently incorporated Spikeinterfaces approach of running Kilosort using a container |
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| -
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8 |
| -The follow pipeline features intermediary tables: |
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| -1. PreProcessing - for preprocessing steps (no GPU required) |
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| - - create recording extractor and link it to a probe |
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| - - bandpass filtering |
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| - - common mode referencing |
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| -2. SIClustering - kilosort (MATLAB) - requires GPU and docker/singularity containers |
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| - - supports kilosort 2.0, 2.5 or 3.0 (https://github.com/MouseLand/Kilosort.git) |
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| -3. PostProcessing - for postprocessing steps (no GPU required) |
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| - - create waveform extractor object |
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| - - extract templates, waveforms and snrs |
18 |
| - - quality_metrics |
| 2 | +The following DataJoint pipeline implements the sequence of steps in the spike-sorting routine featured in the "spikeinterface" pipeline. Spikeinterface was developed by Alessio Buccino, Samuel Garcia, Cole Hurwitz, Jeremy Magland, and Matthias Hennig (https://github.com/SpikeInterface) |
19 | 3 | """
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20 | 4 |
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21 |
| -import pathlib |
22 | 5 | from datetime import datetime
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23 | 6 |
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24 | 7 | import datajoint as dj
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25 | 8 | import pandas as pd
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26 |
| -import probeinterface as pi |
27 | 9 | import spikeinterface as si
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28 | 10 | from element_array_ephys import get_logger, probe, readers
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29 | 11 | from element_interface.utils import find_full_path
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30 | 12 | from spikeinterface import exporters, postprocessing, qualitymetrics, sorters
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31 | 13 |
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| 14 | +from .. import get_logger, probe, readers |
32 | 15 | from . import si_preprocessing
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33 | 16 |
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34 | 17 | log = get_logger(__name__)
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