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Merge pull request #55 from dandi/bf-codespell
codespell: ignore any lines which have data.*base64 - embedded binaries, fix typos introduced in recent PRs
2 parents 7c9ef30 + 18968a0 commit cd963a3

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.codespellrc

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[codespell]
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skip = .git,*.pdf,*.svg
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# all images embedded in .ipynb jsons
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ignore-regex = "image/png": ".*
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# all images and other binaries embedded in .ipynb jsons
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ignore-regex = "image/png": ".*|^ *".*data:\S+;base64.*
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# nd - people just like it
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ignore-words-list = nd

000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/notebooks/Yu-Gutnisky-2016-examples.ipynb

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" <span class=\"djtooltiptext\">in mm, anterior positive, posterior negative</span>\n",
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" </div></th><th><div class=\"djtooltip\">\n",
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" <p id=\"primary\">coordinate_ml</p>\n",
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" <span class=\"djtooltiptext\">in mm, always postive, number larger when more lateral</span>\n",
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" <span class=\"djtooltiptext\">in mm, always positive, number larger when more lateral</span>\n",
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" </div></th><th><div class=\"djtooltip\">\n",
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" <p id=\"primary\">coordinate_dv</p>\n",
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" <span class=\"djtooltiptext\">in mm, always postive, number larger when more ventral (deeper)</span>\n",
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" <span class=\"djtooltiptext\">in mm, always positive, number larger when more ventral (deeper)</span>\n",
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" </div></th><th><div class=\"djtooltip\">\n",
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" <p id=\"nonprimary\">spike_times</p>\n",
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" <span class=\"djtooltiptext\">(s) time of each spike, with respect to the start of session</span>\n",

000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/pipeline/acquisition.py

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'''
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Schema of aquisition information.
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Schema of acquisition information.
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'''
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import re
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import os

000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/pipeline/reference.py

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@@ -93,8 +93,8 @@ class ActionLocation(dj.Manual):
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-> BrainLocation
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-> CoordinateReference
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coordinate_ap: decimal(4,2) # in mm, anterior positive, posterior negative
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coordinate_ml: decimal(4,2) # in mm, always postive, number larger when more lateral
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coordinate_dv: decimal(4,2) # in mm, always postive, number larger when more ventral (deeper)
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coordinate_ml: decimal(4,2) # in mm, always positive, number larger when more lateral
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coordinate_dv: decimal(4,2) # in mm, always positive, number larger when more ventral (deeper)
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"""
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000005/DataJoint/DJ-NWB-Yu-Gutnisky-2016/pipeline/virus.py

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virus: varchar(64) # name of the virus
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---
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-> VirusSource
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virus_lot_number="": varchar(128) # lot numnber of the virus
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virus_lot_number="": varchar(128) # lot number of the virus
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virus_titer=null: float # x10^12GC/mL
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"""
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000006/DataJoint/DJ-NWB-Economo-2018/README.md

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>Michael N. Economo, Sarada Viswanathan, Bosiljka Tasic, Erhan Bas, Johan Winnubst, Vilas Menon, Lucas T. Graybuck, Thuc Nghi Nguyen, Kimberly A. Smith, Zizhen Yao, Lihua Wang, Charles R. Gerfen, Jayaram Chandrashekar, Hongkui Zeng, Loren L. Looger & Karel Svoboda. "Distinct descending motor cortex
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pathways and their roles in movement" (2018) Nature (https://doi.org/10.1038/s41586-018-0642-9)
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The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involed in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution.
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The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involved in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution.
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A ***DataJoint*** data pipeline has been constructed for this study, with the presented data ingested into this pipeline. This notebook demonstrates the queries, processing, and reproduction of several figures from the paper. From the pipeline, export capability to ***NWB 2.0*** format is also available.
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## About the data
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The dataset comprises of extracellular recordings and spike sorted results of the mouse's ALM during a delay-response task. The behavior data includes detailed description of the trial structure (e.g. trial timing, trial instruction, trial response, etc.) and the timing of the lick events (e.g. lick left, lick right onset).
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Original data is publically available at: doi: 10.25378/janelia.7007846
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Original data is publicly available at: doi: 10.25378/janelia.7007846
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The data in original MATLAB format (.mat) have been ingested into a DataJoint data pipeline presented below.
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000006/DataJoint/DJ-NWB-Economo-2018/notebooks/Economo-2018-examples.ipynb

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">Michael N. Economo, Sarada Viswanathan, Bosiljka Tasic, Erhan Bas, Johan Winnubst, Vilas Menon, Lucas T. Graybuck,Thuc Nghi Nguyen, Kimberly A. Smith, Zizhen Yao, Lihua Wang, Charles R. Gerfen, Jayaram Chandrashekar, Hongkui Zeng, Loren L. Looger & Karel Svoboda. \"Distinct descending motor cortex\n",
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"pathways and their roles in movement\" (2018) Nature (https://doi.org/10.1038/s41586-018-0642-9)\n",
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"\n",
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"The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involed in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution. \n",
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"The study identified two types of pyramidal track (PT) neuron in the mouse motor cortex, referred to as PT<sub>upper</sub> and PT<sub>lower</sub>. Further investigation using extracellular recordings in the anterior lateral motor cortex (ALM) during a delay-response task, the study revealed specialized roles for the two neuron types: i) PT<sub>upper</sub> neurons are preferentially involved in motor planning, ii) PT<sub>lower</sub> neurons are more involved in movement execution. \n",
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"\n",
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"A ***DataJoint*** data pipeline has been constructed for this study, with the presented data ingested into this pipeline. This notebook demonstrates the queries, processing, and reproduction of several figures from the paper. From the pipeline, export capability to ***NWB 2.0*** format is also available."
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]
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"\n",
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"The dataset comprises of extracellular recordings and spike sorted results of the mouse's ALM during a delay-response task. The behavior data includes detailed description of the trial structure (e.g. trial timing, trial instruction, trial response, etc.) and the timing of the lick events (e.g. lick left, lick right onset). \n",
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"\n",
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"Original data is publically available at: doi: 10.25378/janelia.7007846\n",
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"Original data is publicly available at: doi: 10.25378/janelia.7007846\n",
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"\n",
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"The data in original MATLAB format (.mat) have been ingested into a DataJoint data pipeline presented below. \n",
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"\n",

000006/DataJoint/DJ-NWB-Economo-2018/pipeline/reference.py

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-> BrainLocation
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-> CoordinateReference
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coordinate_ap: decimal(4,2) # in mm, anterior positive, posterior negative
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coordinate_ml: decimal(4,2) # in mm, always postive, number larger when more lateral
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coordinate_dv: decimal(4,2) # in mm, always postive, number larger when more ventral (deeper)
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coordinate_ml: decimal(4,2) # in mm, always positive, number larger when more lateral
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coordinate_dv: decimal(4,2) # in mm, always positive, number larger when more ventral (deeper)
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"""
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000007/DataJoint/DJ-NWB-Gao-2018/pipeline/acquisition.py

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'''
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Schema of aquisition information.
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Schema of acquisition information.
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'''
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import datajoint as dj
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from pipeline import reference, subject
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-> reference.Hemisphere
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-> reference.CoordinateReference
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photo_stim_coordinate_ap: float # in mm, anterior positive, posterior negative
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photo_stim_coordinate_ml: float # in mm, always postive, number larger when more lateral
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photo_stim_coordinate_dv: float # in mm, always postive, number larger when more ventral (deeper)
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photo_stim_coordinate_ml: float # in mm, always positive, number larger when more lateral
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photo_stim_coordinate_dv: float # in mm, always positive, number larger when more ventral (deeper)
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"""

000007/DataJoint/DJ-NWB-Gao-2018/pipeline/reference.py

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virus: varchar(32) # name of the virus
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---
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-> VirusSource
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virus_lot_number="": varchar(128) # lot numnber of the virus
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virus_lot_number="": varchar(128) # lot number of the virus
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"""
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contents = [{
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'virus': 'AAV2-hSyn-hChR2(H134R)-EYFP',

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