goatpy.io

Functions

parmap(f, X[, nprocs])

Parallel map using joblib (more robust for Jupyter).

getimage(peak, path[, tol, reduce_func])

rd_peaks(fn)

rd_peaks_from_package()

glyco_spatialdata(imzml_path[, peaks_path, tol, ...])

centroids_to_pixel_squares(df[, x_col, y_col, pixel_size])

ihc_spatialdata(ihc_image_path[, channel_names, image_key])

Generate a SpatialData object from a multichannel IHC TIFF/OME-TIFF image.

Module Contents

goatpy.io.parmap(f, X, nprocs=None)[source]

Parallel map using joblib (more robust for Jupyter).

Parameters:

  • f (callable) – Function to apply to each element

  • X (iterable) – Input data

  • nprocs (int, optional) – Number of processes (default: -1, all CPUs)

Returns:

Results in same order as input

Return type:

list

goatpy.io.getimage(peak, path, tol=0.1, reduce_func=sum)[source]
goatpy.io.rd_peaks(fn)[source]
goatpy.io.rd_peaks_from_package()[source]
goatpy.io.glyco_spatialdata(imzml_path, peaks_path=None, tol=0.1, pixel_size=20, reduce_func=sum)[source]
goatpy.io.centroids_to_pixel_squares(df, x_col='x', y_col='y', pixel_size=1.0)[source]
goatpy.io.ihc_spatialdata(ihc_image_path, channel_names=None, image_key='ihc_image')[source]

Generate a SpatialData object from a multichannel IHC TIFF/OME-TIFF image.

Parameters:

  • ihc_image_path (str) – Path to TIFF/OME-TIFF image.

  • channel_names (list, optional) – Names of image channels. Example: [“sc_405”, “CF_488”, “CF_561”, “DIC”]

  • image_key (str) – Name of image key in SpatialData object.

Return type:

SpatialData