This repository is an exploratory resource to accelerate opensource analysis of CosMx® Spatial Molecular Imager (SMI) data. Contained here are and writeups and vignettes addressing a variety of topics discussed when analyzing single-cell spatial data.
anndata is a popular data structure and there are quite a few open-sourced interactive viewer of this data structure that allows non-coders to share the light-weighted data object, visualize and explore the processed data in an interactive view, e.g. cirro viewer, CELLxGENE Annotate viewer
Thus, it's desired to have a tutorial on how to convert AtoMx generated seurat object into a h5ad object that could be used by those viewers. A few customers have also requested about this feature for easier data sharing to their collaborators.
anndata is a popular data structure and there are quite a few open-sourced interactive viewer of this data structure that allows non-coders to share the light-weighted data object, visualize and explore the processed data in an interactive view, e.g. cirro viewer, CELLxGENE Annotate viewer Thus, it's desired to have a tutorial on how to convert AtoMx generated seurat object into a
h5adobject that could be used by those viewers. A few customers have also requested about this feature for easier data sharing to their collaborators.