zoom.prepare.abagen_ctx

zoom.prepare.abagen_ctx(atlas: nibabel.Nifti1Image | Tuple | dict, atlas_info: pandas.DataFrame | PathLike, data_dir: PathLike, donors_threshold: int, gene_stability_threshold: float) → Tuple[pandas.DataFrame, pandas.DataFrame][source]

AHBA processing pipeline optimized for cortical samples.

Parameters:

  • atlas (nibabel.Nifti1Image, tuple or dict) –

    Brain atlas specification. Can be: - A parcellation image in MNI space. - A tuple of GIFTI images in fsaverage5 space. - a dictionary where keys are donor IDs and values are parcellation

    images (or surfaces) in the native space of each donor.

  • atlas_info (pd.DataFrame or os.PathLike) – Filepath to or pre-loaded dataframe containing information about atlas, see abagen document.

  • data_dir (os.PathLike) – Directory where expression data should be downloaded (if it does not already exist) / loaded.

  • donors_threshold (int) – Minimum number of donors required for a region to be included.

  • gene_stability_threshold (float) – Threshold for filtering genes based on differential stability across donors.

Returns:

  • expression (pd.DataFrame) – Processed regional AHBA expression.

  • stability (pd.DataFrame) – Gene-level differential stability.

References

[1] Markello, R. D., Arnatkeviciute, A., Poline, J. B., Fulcher, B. D.,

Fornito, A. & Misic, B. Standardizing workflows in imaging transcriptomics with the abagen toolbox. Elife 10, e72129 (2021).

[2] Dear, R. et al. Cortical gene expression architecture links healthy

neurodevelopment to the imaging, transcriptomics and genetics of autism and schizophrenia. Nat. Neurosci. 27, 1075-1086 (2024).