SimTissue is a python package to simulate in silico smFISH experiment. It can generate 2D or 3D tissue with arbitrary RNA profile and cell shape. Beside it can also sample nuclei position from real experiment and RNA profile from scRNA-seq data.
New version 0.0.3
A complete documentation is available at https://simtissue.readthedocs.io
pip install SimTissue -r requirements.txt
Citation
A point cloud segmentation framework for image-based spatial transcriptomic, Defard et al bioRxiv 2023.12.01.569528; doi: https://doi.org/10.1101/2023.12.01.569528