YangLabHKUST/STitch3D
Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
This tool helps biologists and neuroscientists reconstruct a detailed 3D spatial atlas of an entire organism or tissue from multiple 2D tissue slices and a paired single-cell RNA-sequencing atlas. It identifies 3D functional tissue regions and infers the 3D distribution of various cell types. The output can be used for downstream tasks like analyzing spatial trajectories and identifying genes enriched in specific regions.
No commits in the last 6 months. Available on PyPI.
Use this if you need to build a comprehensive 3D spatial map of tissues or whole organisms by integrating information from multiple 2D spatial transcriptomics datasets and single-cell RNA sequencing data.
Not ideal if you are only working with single 2D tissue slices or do not have complementary single-cell RNA sequencing data, as its strength lies in multi-slice 3D reconstruction and integration.
Stars
70
Forks
6
Language
Python
License
MIT
Category
Last pushed
Nov 20, 2023
Commits (30d)
0
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