Spectral Unmixing Logo

Contents

  • Overview
    • What is bleed-through and why is it a problem?
    • What the package does
    • Stack model and file formats
    • Spectral unmixing model
    • Optional bidirectional unmixing
    • Blind unmixing in the PICASSO family
      • matlab_3c: close port of the original MATLAB algorithm
      • matlab_n: explicit N-channel generalization
      • source_sink_n: explicit source-sink modeling
    • Optional helper modules
    • Reproducibility
    • Modularity and contributions
    • License
    • Citation
    • Where to start
  • Installation
    • Install from PyPI
    • Upgrade an existing installation
    • Developer installation
    • Runtime dependencies
    • Documentation build dependencies
    • Quick verification
  • Usage
    • Example datasets
      • What is included
      • Dataset-to-tutorial mapping
      • Dataset descriptions and provenance
        • PICASSO_examples
        • synthetic_data
        • Gockel_Nieves_Rivera_2026
      • Citation
    • Functionality overview
      • Spectral unmixing workflows
        • unmix(...): directed linear unmixing
          • Forward model
          • Main configuration dimensions
          • Alpha-estimation methods
          • Masking and preprocessing
        • unmix_picasso(...): PICASSO-family blind unmixing
      • Filtering and projection helpers
        • apply_filters(...)
        • match_histograms_across_time(...)
        • max_z_project(...)
      • Registration helpers
      • Visualization helpers
    • Basic unmixing example
      • How to use this tutorial
      • What this tutorial covers
      • Imports
      • Define input and output paths
      • Spectral unmixing with a manually set alpha
      • mean_ratio method
      • linear_fit method
      • corr_min method
      • mi_min method
      • What to change for your own data
    • Full 3D+t unmixing example
      • How to use this tutorial
      • What this tutorial covers
      • Imports
      • Define input and output paths
      • Manually set alpha
      • mean_ratio on a full TZCYX stack
      • linear_fit on a full TZCYX stack
      • corr_min on a full TZCYX stack
      • mi_min on a full TZCYX stack
    • Bidirectional unmixing example
      • How to use this tutorial
      • Core idea
      • Imports
      • Define input and output paths
      • Bidirectional unmixing with fixed coefficients
      • Bidirectional mean_ratio
      • Bidirectional linear_fit
      • Bidirectional corr_min
      • Bidirectional mi_min
      • What to tune most often
    • PICASSO 2-color example
      • How to use this tutorial
      • What this tutorial covers
      • Imports
      • Define input and output paths
      • Inspect the measured channels
      • matlab_n blind unmixing
      • source_sink_n blind unmixing
    • PICASSO 3-color example
      • How to use this tutorial
      • Imports
      • Define input and output paths
      • Inspect the measured channels
      • matlab_n blind unmixing
      • matlab_3c blind unmixing
      • source_sink_n blind unmixing
    • PICASSO 5-color example
      • How to use this tutorial
      • What this tutorial is good for
      • Imports
      • Define input and output paths
      • Inspect the measured channels
      • matlab_n blind unmixing on five channels
      • source_sink_n blind unmixing on five channels
    • 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
        • unmix()
      • spectral_unmixing.unmix_picasso
        • unmix_picasso()
      • spectral_unmixing.unmix_ch0_from_ch1
        • unmix_ch0_from_ch1()
      • spectral_unmixing.estimate_alpha_from_volume
        • estimate_alpha_from_volume()
      • spectral_unmixing.estimate_picasso_unmixing_matrix_from_volume
        • estimate_picasso_unmixing_matrix_from_volume()
      • spectral_unmixing.prepare_source_target_for_alpha
        • prepare_source_target_for_alpha()
      • spectral_unmixing.make_alpha_mask
        • make_alpha_mask()
      • spectral_unmixing.mutual_information_1d
        • mutual_information_1d()
      • spectral_unmixing.apply_filters
        • apply_filters()
      • spectral_unmixing.match_histograms_across_time
        • match_histograms_across_time()
      • spectral_unmixing.max_z_project
        • max_z_project()
      • spectral_unmixing.register_stack
        • register_stack()
      • spectral_unmixing.correct_intra_stack_z_drift
        • correct_intra_stack_z_drift()
      • spectral_unmixing.show_unmixed_channels_in_napari
        • show_unmixed_channels_in_napari()
      • spectral_unmixing.show_all_channels_in_napari
        • show_all_channels_in_napari()
      • spectral_unmixing.convert_time_encoded_stack_to_channel_stack
        • convert_time_encoded_stack_to_channel_stack()
      • spectral_unmixing.report_path_from_output_path
        • report_path_from_output_path()
      • spectral_unmixing.DEFAULT_COLORMAPS
        • DEFAULT_COLORMAPS
  • What’s new?
    • Spectral Unmixing changelog
    • 🚀 spectral-unmixing v0.0.4
      • PICASSO source-sink-N improvements
      • API and reproducibility
      • Scripts and documentation
    • 🚀 spectral-unmixing v0.0.3
      • Unmixing API refinement
      • Documentation
      • Public tutorial datasets
      • Packaging and CI
      • Testing and docs synchronization
    • 🚀 spectral-unmixing v0.0.2
    • 🚀 spectral-unmixing v0.0.1
      • Core unmixing
      • Alpha estimation
      • PICASSO-family blind unmixing
      • Filtering, projection, and registration add-ons
      • I/O and visualization
      • Examples and tutorials
      • Packaging, docs, and testing
  • Contributing
    • Ways to contribute
    • Development workflow
    • Testing
    • Documentation contributions
    • Issues and pull requests
Spectral Unmixing
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