ndx-anatomical-localization Extension for NWB

Provide localization of objects (e.g. electrodes) against a reference image (e.g. CCF).

Often in neurophysiology, you have a set of electrodes or other objects that you want to localize against a reference image. This extension provides a way to store the coordinates of these objects in a standardized way. This is done using a table that stores the coordinates of the objects in a given space (e.g. CCFv3) and a reference to the object that is localized (e.g. an electrode table). This method allows for the storage of multiple localizations in the same file that may correspond to different spaces or registration methods.

Installation

pip install git+https://github.com/catalystneuro/ndx-anatomical-localization.git

Usage

Spaces

Space objects are used to define the coordinate system in which the objects are localized. Each Space object has the following attributes:

• space_name: The name of the space (e.g. "CCFv3")
• origin: The origin of the space (e.g. "bregma")
• units: The units of the space (e.g. "um")
• orientation: A 3-letter string. One of A, P, L, R, S, I for each of x, y, and z (e.g. "RAS").

You can define a custom space by creating a Space object with the desired attributes:

from ndx_anatomical_localization import Space

space = Space(
    name="MySpace",
    space_name="MySpace",
    origin="bregma",
    units="um",
    orientation="RAS",
)

The Allen Institute Common Coordinate Framework v3 is predefined and can be accessed using the get_predefined_space method, or you can define a custom space. You can use the following syntax to use this space:

from ndx_anatomical_localization import Space

space = Space.get_predefined_space("CCFv3")

AnatomicalCoordinatesTable

Once you have a Space object, you can create an AnatomicalCoordinatesTable. The "localized_entity" attribute is a reference to the object that is localized (e.g. an electrode table). x, y, and z columns store the coordinates of the objects in the given space and brain_region allows you to optionally also store the localized brain region. You can also add custom columns to this table, for example to express certainty or quality of the localization.

Localization

The Localization object is used to store the spaces and anatomical coordinates tables in the /general section of the NWB file. Within Localization, you can create multiple Space and AnatomicalCoordinatesTable objects to store localizations of different entities or localizations of the same entity using different methods or spaces.

from pynwb.testing.mock.file import mock_NWBFile
from pynwb.testing.mock.ecephys import mock_ElectrodeTable

from ndx_anatomical_localization import AnatomicalCoordinatesTable, Space, Localization


nwbfile = mock_NWBFile()

localization = Localization()
nwbfile.add_lab_meta_data([localization])

electrodes_table = mock_ElectrodeTable(nwbfile=nwbfile)

space = Space.get_predefined_space("CCFv3")
localization.add_spaces([space])

table = AnatomicalCoordinatesTable(
    name="MyAnatomicalLocalization",
    target=electrodes_table,
    description="Anatomical coordinates table",
    method="SHARP-Track 1.0",
    space=space,
)
[table.add_row(x=1.0, y=2.0, z=3.0, brain_region="CA1", localized_entity=x) for x in range(5)]

localization.add_anatomical_coordinates_tables([table])

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This extension was created using ndx-template.