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EEL mouse sagittal atlas 168 genes spatial RNA data

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posted on 2022-09-21, 15:02 authored by Lars BormLars Borm

Raw RNA locations of the mouse atlas produced by EEL FISH for 168 genes.


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)


RNA .parquet files

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.

Position and gene label for all RNA molecules. 

"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.

"Valid" Boolean column where a 1 means that the molecule is detected inside the tissue section. A zero means the molecule is detected outside.


Tissue polygons .csv files

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.

These polygons were used to generate the "Valid" column. If you want to make your own selection please have a look at the code in: https://github.com/linnarsson-lab/FISHscale/blob/master/FISHscale/utils/inside_polygon.py


Gene colors .pkl file

Pickled Python dictionary with gene colors used in the paper for the mouse atlas.

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