API Reference

The API reference below is generated automatically from the public spectral_unmixing package and its docstrings.

Top-level package

Spectral unmixing utilities for microscopy stacks.

Author: Fabrizio Musacchio Date: June 2026

Public API overview

`unmix`(input_path, output_path[, alpha, ...])	Remove bleed-through from one source channel into one target channel in a TZCYX stack.
`unmix_picasso`(input_path[, output_path, ...])	Perform PICASSO-family multi-channel blind unmixing.
`unmix_ch0_from_ch1`(args, *kwargs)	Backward-compatible wrapper for older code paths.
`estimate_alpha_from_volume`(source, target[, ...])	Estimate a bleed-through coefficient alpha from matching source and target volumes.
`estimate_picasso_unmixing_matrix_from_volume`(...)	Estimate a PICASSO-like blind unmixing matrix from multi-channel image data.
`prepare_source_target_for_alpha`(...[, ...])	Convert, optionally background-correct, and clip source and target volumes.
`make_alpha_mask`(source[, target, ...])	Create a robust mask for alpha estimation.
`mutual_information_1d`(x, y[, bins])	Estimate mutual information between two 1D intensity arrays using a 2D histogram.
`apply_filters`(stack, filters, *[, ...])	Apply one or more filters to a microscopy stack.
`match_histograms_across_time`(stack, *[, ...])	Match each time point to a reference time point using per-channel histogram matching.
`max_z_project`(stack, *[, zrange])	Compute a maximum-intensity projection over the Z axis while preserving `T` and `C`.
`register_stack`(stack, *, registration_channel)	Register a TZCYX stack across time using shifts estimated from Z projections.
`correct_intra_stack_z_drift`(stack, *[, ...])	Correct XY drift between Z slices within each time point of a TZCYX stack.
`show_unmixed_channels_in_napari`(output_path, *)	Show source and corrected target channel from an unmixed stack in a shared napari viewer.
`show_all_channels_in_napari`(stack_path, *[, ...])	Show every channel of a canonical `TZCYX` stack as a separate napari layer.
`convert_time_encoded_stack_to_channel_stack`(...)	Convert a `TZCYX` stack with `T>1` and `C=1` into `T=1` and `C=T`.
`report_path_from_output_path`(output_path)	Return the JSON sidecar path used for reproducibility metadata.
`DEFAULT_COLORMAPS`	Built-in mutable sequence.