@include "rna/_spatial_imaging_stages.mro"

call DETECT_TISSUE(
    downsampled_tissue_image = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/STANDARDIZE_IMAGES/fork0/join-ufe8a67f4d3/files/tissue_hires_image.png",
    scalefactors_json        = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/scalefactors_json.json",
    skip_tissue_detection    = false,
    spot_data_sel            = null,
    loupe_alignment_file     = "/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/V12U06-358-A1_holes.json",
    gpr_data                 = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/GPR_READER/fork0/chnk0-ufe8a67f4d5/files/gpr_data.json",
    spot_positions_list      = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/spot_positions_list.txt",
    fiducial_positions_list  = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ufe8a67f4d9/files/fiducial_positions_list.txt",
    barcode_whitelist        = "visium-v1",
)
