jai-mathur

https://nanostring.com/products/cosmx-spatial-molecular-imager/ffpe-dataset/cosmx-human-lymph-node-ffpe-dataset/ Its this public dataset. fov,cell_ID,cell,x_local_px,y_local_px,x_gl obal_px,y_global_pX,z,target, CellComp 1,0,c_1_1 _0,4256,2904,1 8089.7931257 884,86674.2849349976,0,PNKPNone 1,0,c_1_1_0,4256,3266,1 8089.95405832 93,86311.3562266032,0, N DUFA3,None 1,0,c_1_1_0,4256,3257,1 8089.9024009 705,86320.86912779094,1,GRK6,None 1,0,c_1_1 _0,4256,3295,18089.773257 5735,86282.9367319743,1,LYZ,None 1,0,c_1_1_0,4256,3274,18089.9123350 779,86303.8698832194,2,COX1,None 1,0,c_1_L0,4256,3201,18089.9341901l 43,86376.5319188436,2,TRBC2,None 1,0,c_1_1_0,4256,3328,18089.8328622 182,86249.4945526123,1,SQSTM1,None 1,0,c_1_1_0,4256,3617,18089.7533893...

Hi @dcjones , so this dataset didnt run but I am successfully able to run other cosmx 6k datasets, which have lower number of FOVs (~150). The public dataset if...

@dcjones just so that I can clarify, using the include negative probes in the function call adds the negative probes into the genes matrix of the spatialdata object?

Thank you Rachel. While it seems like the issue was solved for the person in the issue you linked, I am using Proseg 3, and need to somehow figure out...