Tangram

scArches (Single-cell Architecture Surgery) — Python toolkit for reference-based single-cell data integration via transfer learning. Maps query datasets into pre-trained reference atlases using archit

2 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

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

DeepCell — deep learning library for single-cell analysis of biological images using TensorFlow. Provides pretrained models for cell segmentation including Mesmer (multiplexed tissue imaging), nuclear

2 shared topics • 1 shared operation

Geneformer — transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-specific gene network analysis. Supports fine-tuning for cell type classification, gene

2 shared topics • 1 shared operation