EEL mouse sagittal atlas 168 genes RNA spatial data

<strong>Raw RNA locations of the mouse atlas produced by EEL FISH for 168 genes.</strong> <br> RNA files are in the .parquet format which can be opened with FISHscale (https://github.com/linnarsson-lab/FISHscale) or any other parquet file reader (https://arrow.apache.org/docs/index.html) <br> <strong>RNA .parquet files</strong> Seven sagittal sections of the mouse brain with 168 detected genes, sampled at the medial-lateral positions of -140 µm, 600 µm, 1200 µm, 1810 µm, 2420 µm, 3000 µm and 3600 µm measured from the midline. <br> Position and gene label for all RNA molecules. <br> "c_px_microscope_stitched" contains X coordinates. "r_px_microscope_stitched" contians Y coordinates. The unit are pixels with a size of 0.18 micrometer. Multiply by 0.18 to get um scale. <br> <strong>Tissue polygons .csv files</strong> CSV files demarking the sample borders for the 7 mouse atlas sections. -140 µm, 600 µm, 1200 µm, 1810 µm, 2420 µm, 3000 µm, 3600 µm Some RNA molecules are detected outside the tissue area. To remove these you can open the dataset in FISHscale and give it the polygons in the .csv files. If you do not want to use FISHscale, you can use this code to find which points are inside the tissue: https://github.com/linnarsson-lab/FISHscale/blob/master/FISHscale/utils/inside_polygon.py <br> <strong>Gene colors .pkl file</strong> Pickled Python dictionary with gene colors used in the paper for the mouse atlas.