STARmap

Use when working with MENDER (MultilayEred NeighborhooDhood-Encoded Representations), a Python tool for spatial domain identification in multiplexed imaging data. Covers spatial domain segmentation in

3 shared topics • 2 shared operations

Squidpy — spatial single-cell analysis toolkit in the scverse ecosystem for analyzing and visualizing spatial molecular data. Builds spatial neighbor graphs from tissue coordinates (Visium, Xenium, ME

3 shared topics • 2 shared operations

Use when working with BANKSY for spatial transcriptomics clustering that blends each cell's own expression with spatial-neighbor features. Covers SpatialExperiment and SingleCellExperiment pipelines,

2 shared topics • 2 shared operations

Spectre is an R toolkit for high-dimensional single-cell cytometry and imaging analysis, including data import (CSV/FCS), metadata integration, arcsinh/logicle transformation, clustering (FlowSOM, Phe

2 shared topics • 2 shared operations

Tangram — deep learning framework for mapping single-cell and single-nucleus gene expression data onto spatial transcriptomics data. Built on PyTorch and scanpy, Tangram optimizes a probabilistic mapp

2 shared topics • 2 shared operations