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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

STARmap (Spatially-resolved Transcript Amplicon Readout mapping) — in situ spatial transcriptomics method that combines hydrogel-tissue chemistry with sequencing-by-hybridization (SEDAL) for multiplex

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

Cellpose — generalist deep learning algorithm for cellular and nuclear segmentation in microscopy images. Provides GPU-accelerated 2D and 3D instance segmentation using gradient flow representations,

2 shared topics • 1 shared operation

Seurat — comprehensive R toolkit for single-cell genomics enabling QC, normalization (LogNormalize, SCTransform), feature selection, dimensionality reduction (PCA, UMAP, t-SNE), graph-based clustering

2 shared topics • 1 shared operation