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‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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*$py.class
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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wheels/
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*.egg-info/
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.installed.cfg
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*.egg
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.idea/
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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.hypothesis/
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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local_settings.py
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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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scratchpaper.*
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# Jupyter Notebook
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.ipynb_checkpoints
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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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# SageMath parsed files
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*.sage.py
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# dotenv
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./.env
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# virtualenv
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.venv
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venv/
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ENV/
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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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# mypy
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.mypy_cache/
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# datajoint
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dj_local_conf.json
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dj_local_conf_old.json
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# emacs
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**/*~
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**/#*#
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**/.#*
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docker-compose.yml

‎LICENSE

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MIT License
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Copyright (c) 2020 Vathes LLC
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md

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# elements-ephys
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DataJoint Elements for Extracellular Electrophysiology - U24 effort
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# DataJoint Element - Canonical Electrophysiology
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DataJoint Element for electrophysiology.
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This repository features DataJoint pipeline design for extracellular electrophysiology,
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with ***Neuropixels*** probe and ***kilosort*** spike sorting method.
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The pipeline presented here is not a complete pipeline by itself, but rather a modular
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design of tables and dependencies specific to the extracellular electrophysiology workflow.
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This modular pipeline element can be flexibly attached downstream
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to any particular design of experiment session, thus assembling a fully functional
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ephys pipeline.
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## The Pipeline Architecture
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![ephys pipeline diagram](images/attached_ephys_element.png)
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As the diagram depicts, the ephys element starts immediately downstream from ***Session***,
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and also requires some notion of ***Location*** as a dependency for ***InsertionLocation***.
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### The design of probe
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+ ***ProbeType*** - a lookup table specifying the type of Neuropixels probe (e.g. "neuropixels 1.0", "neuropixels 2.0 single-shank")
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+ ***ProbeType.Electrode*** - all electrode and their properties for a particular probe type
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+ An electrode here refers to one recordable electrode site on the Neuropixels probe (e.g. for Neuropixels 1.0, there are 960 sites per shank)
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+ ***Probe*** - record of an actual physical probe, identifiable by some unique ID (e.g. probe's serial number)
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+ ***ElectrodeConfig*** - particular electrode configuration to be used for ephys recording
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+ ***ElectrodeConfig.Electrode*** - corresponding electrodes in ***ProbeType.Electrode*** that are used for recording in this electrode configuration
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(e.g. for Neuropixels 1.0 or 2.0, there can be at most 384 electrodes usable for recording per probe)
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### Extracellular ephys recording
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+ ***ProbeInsertion*** - a surgical insertion of a probe onto the animal.
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Every experimental session consists of one or more ***ProbeInsertion***, with corresponding ***InsertionLocation***
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+ ***EphysRecording*** - each ***ProbeInsertion*** is accompanied by a corresponding ***EphysRecording***,
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specifying the ***ElectrodeConfig*** used for the recording from the ***Probe*** defined in such ***ProbeInsertion***
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+ ***get_npx_data_dir*** method - the class ***EphysRecording*** requires user
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to supply a method to retrieve the directory containing the recorded neuropixels data (e.g. `*.ap.meta`, `*.ap.bin`, etc.),
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where the method's input arguments are the primary attributes identifying one ***EphysRecording***
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### Clusters and spikes
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This ephys element features automatic ingestion for spike sorting results from the ***kilosort*** method.
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+ ***Clustering*** - specify instance(s) of clustering on an ***EphysRecording***, by some ***ClusteringMethod***
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+ ***get_ks_data_dir*** method - the class ***Clustering*** requires user
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to supply a method to retrieve the directory containing the kilosort results,
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where the method's input arguments are the primary attributes identifying one ***Clustering***
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+ ***Unit*** - Identified unit(s) from one ***Clustering***, with associated ***ClusterQualityLabel***
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+ ***UnitSpikeTimes*** - spike times per unit
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+ ***Waveform*** - mean waveform across spikes per unit per recording electrode
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## Usage
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See [this project](https://github.com/vathes/canonical-full-ephys-pipeline) for an example usage of this ephys pipeline element.

‎djephys/__init__.py

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from .ephys import schema as ephys

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