Welcome to STalign’s documentation!
- Overview
- Installation
- What changed in version 2.0.0
- Performance
- Input Data
- 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
- Aligning male and female mouse kidney sections from Cartana
- Functions
LDDMM()LDDMM_3D_to_slice()L_T_from_points()align_cells()analyze3Dalign()backend_info()build_transform()build_transform3D()calculate_tre()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()
- Changes