Spatial alignment of single cell transcriptomic data.

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)

tools and notes for spatial omics

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dime…

A toolkit of spatial transcriptomic analysis.

Toolbox for the analysis of smFISH images.

Spatial Single Cell Analysis in Python

Spatial Transcriptomics Capture Location Deconvolution

Spatial-Linked Alignment Tool

Probabilistic Alignment of Spatial Transcriptomics Experiments

Spatiotemporal modeling of spatial transcriptomics

VT3D: a versatile Visualization Toolbox for 3D spatial transcriptomics atlas

napari: a fast, interactive, multi-dimensional image viewer for python

Interactive visualization of spatial omics data

An open and interoperable data framework for spatial omics data

Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices

A Toolbox for Spatial Transcriptomics Analysis

Analyzing cellular niches in spatial transcriptomics data

Spatial omics analysis toolbox

A novel machine learning pipeline to analyse spatial transcriptomics data

Raw format to OME-TIFF converter

SpaceX: Gene Co-expression Network Estimation for Spatial Transcriptomics

Biologically-informed deep learning for cell segmentation of subcelluar spatial transcriptomics data

BANKSY: spatial clustering

scTM: A package for topic modelling in transcriptomics data