mCNS-atlas

Code and implementation for the 'Spatial Atlas of the Mouse Central Nervous System at Molecular Resolution'.

1. STARmap PLUS data processing
2. Cell segmentation and cell typing
3. Tissue domain analysis (spatial_integration)
4. CCF registration
5. Imputation
6. AAV.PHP.eB circular RNA barcode analysis

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Other Info

Citation

If you find mCNS-atlas useful for your work, please cite our paper:

Shi, H., He, Y., Zhou, Y., Huang, J., Maher, K., Wang, B., Tang, Z., Luo, S., Tan, P., Wu, M. and Lin, Z., 2023. Spatial atlas of the mouse central nervous system at molecular resolution. Nature, pp.1-10.

Contributor

Yichun He, Jiahao Huang, Kamal Maher, Brandon Wang, Hailing Shi, Xin Tang

Acknowledgement

The following packages and software were used in data analysis: UCSF ChimeraX 1.0, ImageJ 1.51, MATLAB R2019b, R 4.0.4, Rstudio 1.4.1106, Jupyter Notebook 6.0.3, Anaconda 2-2-.02, h5py 3.1.0, hdbscan 0.8.36, hdf5 1.10.4, matplotlib 3.1.3, seaborn 0.11.0, scanpy 1.6.0, numpy 1.19.4, scipy 1.6.3, pandas 1.2.3, scikit-learn 0.22, umap-learn0.4.3, pip 21.0.1, numba 0.51.2, tifffile 2020.10.1, scikit-image 0.18.1, itertools 8.0.0.