STalign Logo
  • Overview
  • Installation & Import
  • Input Data
  • Usage
  • Tutorials
  • Functions
STalign
  • Welcome to STalign’s documentation!
  • View page source

Welcome to STalign’s documentation!

  • Overview
  • Installation & Import
    • Installation using pip
    • Installation using Pipfile from source
    • Import
  • Input Data
    • single-cell resolution ST alignment
    • single-cell and spot-resolution ST alignment
    • 3D-2D alignment
  • Usage
  • Tutorials
    • Aligning two coronal sections of adult mouse brain from MERFISH
    • Aligning partially matched, serial, single-cell resolution breast cancer spatial transcriptomics data from Xenium
    • Aligning single-cell resolution breast cancer spatial transcriptomics data to corresponding H&E staining image from Xenium
    • Aligning partially matched coronal sections of adult mouse brain from Xenium and STARmap PLUS
    • Aligning adult mouse coronal brain sections with the Allen Brain Altas
    • Aligning partial coronal brain sections with the Allen Brain Altas
    • Aligning single-cell resolution spatial transcriptomics data to H&E staining image from Visium
    • Aligning heart ST data from ISS
  • Functions
    • LDDMM()
    • LDDMM_3D_to_slice()
    • L_T_from_points()
    • analyze3Dalign()
    • build_transform()
    • build_transform3D()
    • clip()
    • download_aba_image_labels()
    • download_aba_ontology()
    • extent_from_x()
    • interp()
    • interp3D()
    • make_scree()
    • normalize()
    • plot_brain_regions()
    • plot_subset_brain_regions()
    • rasterize()
    • rasterizePCA()
    • rasterize_with_signal()
    • saveRasters()
    • to_A()
    • to_A_3D()
    • transform_image_source_to_target()
    • transform_image_source_with_A()
    • transform_image_target_to_source()
    • transform_points_source_to_target()
    • transform_points_target_to_source()
    • v_to_phii()
    • v_to_phii_3D()
Next

© Copyright 2023, JEFworks Lab.

Built with Sphinx using a theme provided by Read the Docs.