Hello!

I have some seqFISH data from Spatial Genomics generated by their 'genePS' system. I was wondering if anyone had some code to import this data into a SpatialExperiment S4 R/Bioconductor class object? It seems like the import functions were developed for the 10X Visium.

I did find a tutorial from a Hackathon, but it was for multimodal data and required the data to be run through smfish-hmrf, which would be ideal normally. I don't have the extra information to use it.

The output data per ROI is in three CSV files which are structured like this:

*_CellCoordinates.csv
label,area,center_x,center_y
1,4293,23720,1512
2,6549,24498,1530
3,2670,23152,1514
4,4639,23537,1515

*_CellxGene.csv
    ITGB1   NR4A1   THBS1   HIF1A   ******    ID2   CD37    DUSP2   ETS1  (600 gene entries)    
1   0   0   2   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   0   0   0   0   0   0   0   0   
2   0   1   0   0   0   0   0   0   0   0   0   3   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   
3   0   0   1   0   0   0   0   1   1   0   0   1   0   0   1   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   0   1   0   0   1   0   1   0   0   0   1   0   0   0   0   

*TranscriptList.csv
name,x,y,z
ITGB1,13841,3777,1
ITGB1,13850,3773,1
ITGB1,14866,3292,1
ITGB1,14894,3774,1

This was all I was given to work with (so far). I will track down the images for all 7 ROI. Any advice or information that you can share with me is greatly appreciated. Thank you.