Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add documentation about duplicated metadata in Electrodes #442

Merged
merged 2 commits into from
Apr 4, 2024
Merged

Add documentation about duplicated metadata in Electrodes #442

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e0f2a95
add documentation about duplicated metadata
h-mayorquin Apr 2, 2024
5b4cd13
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions docs/best_practices/ecephys.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -58,6 +58,12 @@ For relative position of an electrode on a probe, use ``rel_x``, ``rel_y``, and
that are close enough to share a neuron.


Avoid Duplication of Metadata
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

The ``ElectrodeTable`` should not contain redundant information that is present somewhere else within the :ref:`nwb-schema:sec-NWBFile` . Avoid adding columns to the `ElectrodeTable` that correspond to properties of the :ref:`nwb-schema:sec-ElectricalSeries` such as ``unit``, ``offsets`` or ``channel gains`` These properties should be stored in the corresponding attributes of the :ref:`nwb-schema:sec-ElectricalSeries` object.

As a concrete example, the package objects from the `SpikeInterface <https://spikeinterface.readthedocs.io/en/latest/>`__ package contain two properties named ``gain_to_uv`` and ``offset_to_uv`` that are used to convert the raw data to microvolts. These properties should not be stored in the `ElectrodeTable` but rather in the ``ElectricalSeries`` object as ``channel_conversion`` and ``offset`` respectively.

Units Table
-----------
Expand Down
6 changes: 6 additions & 0 deletions docs/best_practices/general.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,3 +68,9 @@ Empty Strings
Required free-text fields for neurodata types should not use placeholders such as empty strings (`""`), ``"no description"``, or ``"PLACEHOLDER"``. For example, the :py:attr:`description` field should always richly describe that particular neurodata type and its interpretation within the experiment.

Many attributes of neurodata types in NWB are optional details to include. It is not necessary, therefore, to use placeholders for these attributes. Instead, they should not be specified at all.


Avoid Duplication of Metadata
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Avoid duplication of metadata across different objects. If a piece of metadata is shared between multiple objects, consider creating a separate object to store that metadata and linking to it from the other objects. This will help to keep the metadata consistent and reduce the risk of errors when updating the metadata.
Loading