Spectral Unmixing Documentationο
spectral-unmixing is a Python package for spectral bleed-through correction in microscopy stacks. It provides linear two-channel unmixing workflows, optional bidirectional correction, and PICASSO-family blind-unmixing workflows for multi-channel data.
The package is built around microscopy stacks in canonical TZCYX order and
uses OMIO for I/O. This means that
the workflows are not restricted to TIFF files alone, but can be applied to any
microscopy format currently supported by OMIO.
In addition to the core unmixing functions, the package includes optional helpers for filtering, projection, time registration, intra-stack z-drift correction, and napari-based inspection.
Contents
- Overview
- Installation
- Usage
- Example datasets
- Functionality overview
- Basic unmixing example
- Full 3D+t unmixing example
- Bidirectional unmixing example
- PICASSO 2-color example
- PICASSO 3-color example
- PICASSO 5-color example
- Filtering, registration, and projection helper example
- How to use this tutorial
- What this tutorial covers
- Imports
- Define input and output paths
- Load the stack
- Correct intra-stack z-drift
- Register the stack across time
- Match histograms across time
- Filter the registered stack
- Project along z
- Filter the projected stack again
- Save the processed stack
- Fine-tuning
- How to read the tutorials
- Recommended starting point
- API Reference
- Top-level package
- Public API overview
- spectral_unmixing.unmix
- spectral_unmixing.unmix_picasso
- spectral_unmixing.unmix_ch0_from_ch1
- spectral_unmixing.estimate_alpha_from_volume
- spectral_unmixing.estimate_picasso_unmixing_matrix_from_volume
- spectral_unmixing.prepare_source_target_for_alpha
- spectral_unmixing.make_alpha_mask
- spectral_unmixing.mutual_information_1d
- spectral_unmixing.apply_filters
- spectral_unmixing.match_histograms_across_time
- spectral_unmixing.max_z_project
- spectral_unmixing.register_stack
- spectral_unmixing.correct_intra_stack_z_drift
- spectral_unmixing.show_unmixed_channels_in_napari
- spectral_unmixing.show_all_channels_in_napari
- spectral_unmixing.convert_time_encoded_stack_to_channel_stack
- spectral_unmixing.report_path_from_output_path
- spectral_unmixing.DEFAULT_COLORMAPS
- Whatβs new?
- Contributing