https://github.com/datajoint/element-event
DataJoint Element for event-based behavior experiments
https://github.com/datajoint/element-event
behavior neuroscience
Last synced: 2 months ago
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DataJoint Element for event-based behavior experiments
- Host: GitHub
- URL: https://github.com/datajoint/element-event
- Owner: datajoint
- License: mit
- Created: 2021-11-05T22:28:10.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2025-02-19T05:30:40.000Z (4 months ago)
- Last Synced: 2025-04-27T16:20:05.399Z (2 months ago)
- Topics: behavior, neuroscience
- Language: Python
- Homepage: https://datajoint.com/docs
- Size: 1.01 MB
- Stars: 1
- Watchers: 8
- Forks: 18
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
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README
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# DataJoint Element - Experimental trials
+ `element-event` features a DataJoint pipeline design for event, trial, and block management.
+ `element-event` is not a complete workflow by itself, but rather a modular design of tables and dependencies.
+ `element-event` can be flexibly attached to any DataJoint workflow.
+ See the [Element Event documentation](https://elements.datajoint.org/description/event/) for the background information and development timeline.
+ For more information on the DataJoint Elements project, please visit https://elements.datajoint.org. This work is supported by the National Institutes of Health.
## Element architecture
In diagram below, ***BehaviorRecording*** table starts immediately downstream from
***Session***. Recordings can be segmented into both trials, which are assumed to have
duration, and events, which may be instantaneous. Researchers may find one or both appropriate for their particular paradigm. A set of trials can be further organized into
blocks, representing a larger span of time. We provide an
[example workflow](https://github.com/datajoint/workflow-trial/) with a
[pipeline script](https://github.com/datajoint/workflow-trial/blob/main/workflow_trial/pipeline.py)
that models combining this Element with the corresponding
[Element-Session](https://github.com/datajoint/element-session).
### Trial & Event Schemas
## Installation
+ Install `element-event`
```
pip install element-event
```
+ Upgrade `element-event` previously installed with `pip`
```
pip install --upgrade element-event
```
## Usage
### Element activation
To activate the `element-event`, one need to provide:
1. Schema names for the event or trial module
2. Upstream Session table: A set of keys identifying a recording session (see [
Element-Session](https://github.com/datajoint/element-session)).
3. Utility functions. See
[example definitions here](https://github.com/datajoint/workflow-trial/blob/main/workflow_trial/paths.py)
For more detail, check the docstring of the `element-event`:
```python
from element_event import event, trial
help(event.activate)
help(trial.activate)
```
### Element usage
+ See the
[workflow-calcium-imaging](https://github.com/datajoint/workflow-calcium-imaging),
[workflow-array-ephys](https://github.com/datajoint/workflow-array-ephys), and
[workflow-miniscope](https://github.com/datajoint/workflow-miniscope)
repositories for example usages of `element-event`.
## Citation
+ If your work uses DataJoint and DataJoint Elements, please cite the respective Research Resource Identifiers (RRIDs) and manuscripts.
+ DataJoint for Python or MATLAB
+ Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AS, Tolias AS. DataJoint: managing big scientific data using MATLAB or Python. bioRxiv. 2015 Jan 1:031658. doi: https://doi.org/10.1101/031658
+ DataJoint ([RRID:SCR_014543](https://scicrunch.org/resolver/SCR_014543)) - DataJoint for `` (version ``)
+ DataJoint Elements
+ Yatsenko D, Nguyen T, Shen S, Gunalan K, Turner CA, Guzman R, Sasaki M, Sitonic D, Reimer J, Walker EY, Tolias AS. DataJoint Elements: Data Workflows for Neurophysiology. bioRxiv. 2021 Jan 1. doi: https://doi.org/10.1101/2021.03.30.437358
+ DataJoint Elements ([RRID:SCR_021894](https://scicrunch.org/resolver/SCR_021894)) - Element Event (version ``)