README.md

Glioblastoma is spatially organized by neurodevelopmental programs and a glial-like wound healing response

(Mossi Albiach & Janusauskas et al. 2023, in review).

Download the m-cell gene expression matrix with polygons and coordinates

Gene expression matrix.

We use the FISHscale pipeline for unsupervised cell-free segmentation (m-states). We use the FISHspace software for plotting m-cells and further analysis. FISHspace software is based on stlearn (https://stlearn.readthedocs.io/en/latest/) with added plotting and processing functions.

Download the molecules spatial coordinates

For the visualization of Molecules Spatial Coordinates we recommend to use FISHscale. FISHscale visualizer is based upon Open3D, allowing for blazing fast visualization of datasets of millions of RNA molecules.