Conversion Scripts

The following directory contains examples to convert author-published results into the spatial schema. The majority of the scripts are very simple. Each script is named as follows and has at minimum the following contents:

<assay_name>_<first_author>_<year>_<journal>_<short_description>.py

1. Link to original manuscript or preprint, if available, else data attribution information
2. Checklist of available data, including:

1. cell (or region) x gene count matrix
2. transcript locations (if appropriate)
3. cell locations in polygons or masks

4. Instructions to load and convert data into required format, including any information acquired via direct communications with authors.

Spatially resolved, highly multiplexed RNA profiling in single cells

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

Spatially resolved, highly multiplexed RNA profiling in single cells

Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas

spatial organization of the somatosensory cortex revealed by cyclic smfish