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notebooks/tutorial.ipynb

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"source": [
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"# DataJoint Elements for Array Electrophysiology with NeuroPixels\n",
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"\n",
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"#### Open-source Data Pipeline for Processing and Analyzing Extracellular Electrophysiology Datasets\n",
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"#### Open-source data pipeline for processing and analyzing extracellular electrophysiology datasets.\n",
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"\n",
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"Welcome to the tutorial for the DataJoint Element for extracellular array electrophysiology. This\n",
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"tutorial aims to provide a comprehensive understanding of the open-source data pipeline\n",
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"created using `element-array-ephys`.\n",
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"\n",
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"This package is designed to seamlessly process and ingest extracellular electrophysiology\n",
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"This package is designed to seamlessly process, ingest, and track extracellular electrophysiology\n",
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"data, along with its associated probe and recording metadata. By the end of this\n",
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"tutorial you will have a clear grasp on setting up and integrating `element-array-ephys`\n",
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"into your specific research projects and lab. \n",
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"and manage sessions of array electrophysiology data, including spike sorting results and\n",
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"unit-level visualizations. \n",
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"\n",
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"The results of this Element example can be combined with **other modalities** to create\n",
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"a complete customizable data pipeline for your specific lab or study. For instance, you\n",
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"The results of this Element can be combined with **other modalities** to create\n",
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"a complete, customizable data pipeline for your specific lab or study. For instance, you\n",
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"can combine `element-array-ephys` with `element-calcium-imaging` and\n",
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"`element-deeplabcut` to characterize the neural activity along with markless\n",
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"pose-estimation during behavior.\n",
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"If the tutorial is run in Codespaces, there is a local database private to you for\n",
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"experimentation. Let's connect to the database server."
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"If the tutorial is run in Codespaces, a private, local database server is created and\n",
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"made available for you. This is where we will insert and store our processed results.\n",
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"Let's connect to the database server."
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]
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},
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"As evident from the diagram, this data pipeline encompasses tables associated with\n",
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"recording and probe metadata, results of clustering, and optional curation of clustering\n",
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"results. A few tables, such as `subject.Subject` or `session.Session`,\n",
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"while important for a complete pipeline, fall outside the scope of `element-array-ephys`\n",
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"while important for a complete pipeline, fall outside the scope of the `element-array-ephys`\n",
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"tutorial, and will therefore, not be explored extensively here. The primary focus of\n",
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"this tutorial will be on the `probe` and `ephys` schemas.\n",
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"\n",

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