Spage2vec is an unsupervised segmentation free approach for decrypting the spatial transcriptomic heterogeneity of complex tissues at subcellular resolution. Spage2vec represents the spatial transcriptomic landscape of tissue samples as a graph and leverage powerful machine learning graph representation technique to create a lower dimensional representation of local spatial gene expression. Here we visualize spage2vec localized gene expression signatures of different spatial transcriptomic datasets.
We thank Mats Nilsson, Sten Linnarsson and Xiaowei Zhuang for making their datasets publicly available.

TissUUmaps interactive viewer 1:
In situ sequencing mouse brain hippocampal area CA1
Qian, X., Harris, K. D., Hauling, T., Nicoloutsopoulos, D., Muñoz-Manchado, A. B., Skene, N., … & Nilsson, M. (2020). Probabilistic cell typing enables fine mapping of closely related cell types in situ. Nature methods, 17(1), 101-106.

TissUUmaps interactive viewer 2:
osmFISH mouse brain somatosensory cortex
Codeluppi, S., Borm, L. E., Zeisel, A., La Manno, G., van Lunteren, J. A., Svensson, C. I., & Linnarsson, S. (2018). Spatial organization of the somatosensory cortex revealed by osmFISH. Nature methods, 15(11), 932-935.

TissUUmaps interactive viewer 3:
MERFISH mouse brain hypothalamic preoptic area
Moffitt, J. R., Bambah-Mukku, D., Eichhorn, S. W., Vaughn, E., Shekhar, K., Perez, J. D., … & Zhuang, X. (2018). Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science, 362(6416), eaau5324.

TissUUmaps interactive viewer 4:
MERFISH human fibroblast cells (IMR90)
Chen, K. H., Boettiger, A. N., Moffitt, J. R., Wang, S., & Zhuang, X. (2015). Spatially resolved, highly multiplexed RNA profiling in single cells. Science, 348(6233), aaa6090.

Data and code availability: Spatial gene expression data are available in Zenodo database at https://doi.org/10.5281/zenodo.3897401. Source code for reproducing analysis results and figures is available in Zenodo database at http://www.doi.org/10.5281/zenodo.4030404.