probe_geometry.py

NXT3000 = [1, 70, 0, 53, 53, 0, 15, 128, 128] module-attribute

Electrode coordinate system - from Bill Karsh (https://github.com/billkarsh/SpikeGLX/blob/master/Markdown/Metadata_30.md)

The X-origin is the left edge of the shank The Y-origin is the center of the bottom-most elecrode row (closest to the tip)

build_electrode_layouts(probe_type, site_count_per_shank, col_spacing=None, row_spacing=None, row_offset=None, col_count_per_shank=1, shank_count=1, shank_spacing=None, y_origin='bottom', as_dataframe=False)

Builds electrode layouts.

Parameters:

Name	Type	Description	Default
probe_type	str	probe type (e.g., "neuropixels 1.0 - 3A").	required
site_count_per_shank	int	site count per shank.	required
col_spacing	float	(um) horizontal spacing between sites. Defaults to None (single column).	None
row_spacing	float	(um) vertical spacing between columns. Defaults to None (single row).	None
row_offset	list	(um) per-row offset spacing. Defaults to None.	None
col_count_per_shank	int	number of column per shank. Defaults to 1 (single column).	1
shank_count	int	number of shank. Defaults to 1 (single shank).	1
shank_spacing	float	(um) spacing between shanks. Defaults to None (single shank).	None
y_origin	str	{"bottom", "top"}. y value decrements if "top". Defaults to "bottom".	'bottom'
as_dataframe	bool	if True, returns as pandas DataFrame, otherwise as list of dict	False

Source code in element_array_ephys/readers/probe_geometry.py

def build_electrode_layouts(
    probe_type: str,
    site_count_per_shank: int,
    col_spacing: float = None,
    row_spacing: float = None,
    row_offset: list = None,
    col_count_per_shank: int = 1,
    shank_count: int = 1,
    shank_spacing: float = None,
    y_origin="bottom",
    as_dataframe=False,
) -> list[dict]:
    """Builds electrode layouts.

    Args:
        probe_type (str): probe type (e.g., "neuropixels 1.0 - 3A").
        site_count_per_shank (int): site count per shank.
        col_spacing (float): (um) horizontal spacing between sites. Defaults to None (single column).
        row_spacing (float): (um) vertical spacing between columns. Defaults to None (single row).
        row_offset (list): (um) per-row offset spacing. Defaults to None.
        col_count_per_shank (int): number of column per shank. Defaults to 1 (single column).
        shank_count (int): number of shank. Defaults to 1 (single shank).
        shank_spacing (float): (um) spacing between shanks. Defaults to None (single shank).
        y_origin (str): {"bottom", "top"}. y value decrements if "top". Defaults to "bottom".
        as_dataframe (bool): if True, returns as pandas DataFrame, otherwise as list of dict
    """
    row_count = int(site_count_per_shank / col_count_per_shank)
    x_coords = np.tile(
        np.arange(0, (col_spacing or 1) * col_count_per_shank, (col_spacing or 1)),
        row_count,
    )
    y_coords = np.repeat(np.arange(row_count) * (row_spacing or 1), col_count_per_shank)

    if row_offset is None:
        row_offset = np.zeros_like(x_coords)
    else:
        assert len(row_offset) == row_count
        row_offset = np.tile(row_offset, col_count_per_shank)
    x_coords = x_coords + row_offset

    shank_cols = np.tile(range(col_count_per_shank), row_count)
    shank_rows = np.repeat(range(row_count), col_count_per_shank)

    electrode_layout = [
        {
            "probe_type": probe_type,
            "electrode": (site_count_per_shank * shank_no) + e_id,
            "shank": shank_no,
            "shank_col": c_id,
            "shank_row": r_id,
            "x_coord": x + (shank_no * (shank_spacing or 1)),
            "y_coord": {"top": -y, "bottom": y}[y_origin],
        }
        for shank_no in range(shank_count)
        for e_id, (c_id, r_id, x, y) in enumerate(
            zip(shank_cols, shank_rows, x_coords, y_coords)
        )
    ]

    return pd.DataFrame(electrode_layout) if as_dataframe else electrode_layout