PyNutil.xy_to_coords#

PyNutil.xy_to_coords(coordinates, registration, atlas, return_orientation='asr')[source]#

Transform image-space coordinates into atlas space.

Parameters:

  • coordinates (pd.DataFrame) – A pandas.DataFrame containing coordinates and section metadata. Must contain the columns X, Y, image_width, image_height, and section number.

  • registration (RegistrationData) – Registration data returned by PyNutil.read_alignment().

  • atlas (Union[AtlasData, BrainGlobeAtlas]) – Atlas definition to use for labeling. This may be an AtlasData instance or a BrainGlobe atlas object.

  • return_orientation (3-letter BrainGlobe orientation string (e.g. "asr",) – “ras”). Defaults to “asr” (internal orientation).

Returns:

Atlas-space points, object placeholders, and region-area summaries derived from the input coordinates. In coordinate mode, result.points contains the transformed atlas-space coordinates and labels, while result.objects mirrors the same coordinates for downstream quantification and export code.

Return type:

ExtractionResult

Examples

Transform pre-extracted image-space coordinates:

>>> import pandas as pd
>>> from brainglobe_atlasapi import BrainGlobeAtlas
>>> atlas = BrainGlobeAtlas("allen_mouse_25um")
>>> registration = read_alignment("path/to/alignment.json")
>>> df = pd.read_csv("path/to/coordinates.csv")
>>> result = xy_to_coords(df, registration, atlas)
>>> result.points.points.shape
(N, 3)
>>> result.section_filenames
[]