Draw polygon from flatfile

[Lingxiao-LIU]

How to use the AtoMx export Flatfiles/SeuratObject to draw polygons and overlay them with transcripts? (where are the xy locations of individual transcripts stored?)

[eveilyeverafter]

Take a look at the polygons csv file

[Lingxiao-LIU]

Take a look at the polygons csv file

I read the polygon file, but it does not contain any transcript information, only fov and cell ID. I don't know what the xy locations represents.

[eveilyeverafter]

There isn't a single flat file that has both types of data. The polygons file contains the vertices of the cells. When exporting the flat files, you should also see an option to export the transcripts data which have the spatial coordinates of individual transcripts. I don't believe your screenshot shows that file.

If you create the napari zarr files, you can also view the polygons and transcripts using that method.