nuclei (1 file: tile, cell, x, y, seq, ignored; ssuming 468 tiles per file, with header):

nuclei assignment (in-situ tile, cell, x, y, area, pheno tile, cell, x, y, area; with header):

phenotype (pheno tile, cell, x, y, whatever; with header):

guide library (gene, sequence; must perfectly match nuclei sequences, no header):