API Reference

This page documents the public API of the bioio package.

Core Classes

BioImage(image[, reader, ...])	BioImage takes microscopy image data types (files or arrays) of varying dimensions ("ZYX", "TCZYX", "CYX") and reads them as consistent 5D "TCZYX" ("Time-Channel-Z-Y-X") ordered array(s).
StandardMetadata([binning, column, ...])	A simple container for embedded metadata fields.
Writer()	A small class to build standardized image writer functions.

Types and Aliases

ArrayLike
DimensionProperties(T, C, Z, Y, X)	Container for dimension properties for all supported dims.
MetaArrayLike
Scale(T, C, Z, Y, X)	Per-dimension scale factors for T, C, Z, Y, X.
TimeInterval
ImageLike
PathLike
PhysicalPixelSizes(Z, Y, X)	Physical pixel sizes along the Z, Y, and X axes.

Enums and Dimensions

DimensionNames()
Dimensions(dims, shape)	A general object for managing the pairing of dimension name and dimension size.

Utilities

plugin_feasibility_report(image[, ...])

Generate a feasibility report for each plugin, determining if it can handle the specified image.