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‎examples/exploring_data/data_download.ipynb‎

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"c3f58136-2198-4a39-bde0-e2a8cf112a56\n"
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]
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}
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],
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"source": [
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"# Each session is represented by a unique experiment id (eID)\n",
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"print(sessions[0],)"
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"outputs": [
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{
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"output_type": "stream",
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"text": [
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"2021_Q1_IBL_et_al_Behaviour\n",
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"https://doi.org/10.7554/eLife.63711\n",
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"\n",
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"2021_Q2_PreRelease\n",
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"https://figshare.com/articles/online_resource/Spike_sorting_pipeline_for_the_International_Brain_Laboratory/19705522/3\n",
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"\n",
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"2021_Q2_Varol_et_al\n",
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"https://doi.org/10.1109/ICASSP39728.2021.9414145\n",
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"\n",
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"2021_Q3_Whiteway_et_al\n",
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"https://doi.org/10.1371/journal.pcbi.1009439\n",
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"\n",
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"2022_Q2_IBL_et_al_RepeatedSite\n",
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"https://doi.org/10.1101/2022.05.09.491042\n",
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"\n",
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"2022_Q3_IBL_et_al_DAWG\n",
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"https://doi.org/10.1101/827873\n",
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"\n",
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"2022_Q4_IBL_et_al_BWM\n",
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"https://figshare.com/articles/preprint/Data_release_-_Brainwide_map_-_Q4_2022/21400815\n",
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"\n",
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"2023_Q1_Biderman_Whiteway_et_al\n",
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"\n",
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"\n",
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"2023_Q1_Mohammadi_et_al\n",
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"\n",
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"\n",
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"2023_Q3_Findling_Hubert_et_al\n",
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"https://doi.org/10.1101/2023.07.04.547684\n",
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"\n",
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"2023_Q4_Bruijns_et_al\n",
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"\n",
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"\n",
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"2023_Q4_IBL_et_al_BWM_2\n",
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"\n",
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"\n",
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"2023_Q4_IBL_et_al_BWM_passive\n",
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"\n",
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"\n",
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"2024_Q2_Blau_et_al\n",
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"\n",
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"\n",
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"2024_Q2_IBL_et_al_BWM_iblsort\n",
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"Spike sorting output with ibl-sorter 1.7.0 for BWM\n",
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"\n",
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"2024_Q2_IBL_et_al_RepeatedSite\n",
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"https://doi.org/10.1101/2022.05.09.491042\n",
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"\n",
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"2024_Q3_Pan_Vazquez_et_al\n",
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"\n",
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"\n",
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"2025_Q1_IBL_et_al_BWM_wheel_patch\n",
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"62 patched sessions with reversed wheel polarity\n",
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"\n",
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"Brainwidemap\n",
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"\n",
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"\n",
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"RepeatedSite\n",
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"\n",
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"\n"
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]
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}
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],
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"source": [
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"# List and print all tags in the public database\n",
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"tags = {t['name']: t['description'] for t in one.alyx.rest('tags', 'list') if t['public']}\n",
@@ -218,7 +293,7 @@
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Files downloaded to /Users/admin/Downloads/ONE/openalyx.internationalbrainlab.org/churchlandlab_ucla/Subjects/MFD_09/2023-10-19/001/alf\n"
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]
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}
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],
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"source": [
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"# Find an example session with trials data\n",
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"eid, *_ = one.search(project='brainwide', datasets='_ibl_trials.table.pqt')\n",
@@ -273,13 +356,98 @@
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"outputs": [
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{
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"text": [
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/_ibl_log.info_pykilosort.log; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/_kilosort_whitening.matrix.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/_phy_spikes_subset.channels.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/_phy_spikes_subset.spikes.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/_phy_spikes_subset.waveforms.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/channels.brainLocationIds_ccf_2017.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/channels.localCoordinates.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/channels.mlapdv.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/channels.rawInd.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-03-22#/clusters.amps.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/clusters.channels.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-03-22#/clusters.depths.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/clusters.metrics.pqt; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/clusters.peakToTrough.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/clusters.uuids.csv; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-03-22#/clusters.waveforms.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/clusters.waveformsChannels.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/drift.times.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/drift.um.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-03-22#/drift_depths.um.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/spikes.amps.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-03-22#/spikes.clusters.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/spikes.depths.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-03-22#/spikes.samples.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-05-06#/spikes.templates.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/spikes.times.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/#2024-03-22#/templates.amps.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/templates.waveforms.npy; using most recent\n",
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" warnings.warn(\n",
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"/Users/admin/int-brain-lab/ONE/one/util.py:406: ALFWarning: No default revision for dataset alf/probe00/pykilosort/templates.waveformsChannels.npy; using most recent\n",
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"100%|█████████████████████████████████████████| 15/15.0 [00:08<00:00, 1.71it/s]\n",
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"100%|███████████████████████████████████████████| 3/3.0 [00:01<00:00, 1.96it/s]\n",
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"100%|███████████████████████████████████████████| 3/3.0 [00:01<00:00, 1.90it/s]\n",
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"100%|███████████████████████████████████████████| 3/3.0 [00:01<00:00, 1.97it/s]\n",
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"100%|███████████████████████████████████████████| 3/3.0 [00:01<00:00, 1.98it/s]\n",
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"100%|█████████████████████████████████████████| 16/16.0 [00:09<00:00, 1.74it/s]"
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]
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},
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"text": [
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"Files downloaded to /Users/admin/Downloads/ONE/openalyx.internationalbrainlab.org/churchlandlab_ucla/Subjects/MFD_09/2023-10-19/001/alf/probe00/pykilosort/#2024-05-06#\n"
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]
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],
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"# Find an example session with spike data\n",
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"eid, *_ = one.search(project='brainwide', dataset='spikes', task='ephys')\n",
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"eid, *_ = one.search(project='brainwide', datasets='spikes.times.npy', task='ephys')\n",
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"datasets = one.list_datasets(eid, collection='alf/probe*')\n",
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