@include "rna/_spatial_imaging_stages.mro"

call DETECT_TISSUE(
    downsampled_tissue_image = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/STANDARDIZE_IMAGES/fork0/join-ue5873dadfe/files/tissue_hires_image.png",
    scalefactors_json        = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/scalefactors_json.json",
    skip_tissue_detection    = false,
    spot_data_sel            = null,
    loupe_alignment_file     = "/gpfs/home/jw7078/ST-399/V12D12-399-A1.json",
    gpr_data                 = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/GPR_READER/fork0/chnk0-ue5873dae00/files/gpr_data.json",
    spot_positions_list      = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/spot_positions_list.txt",
    fiducial_positions_list  = "/gpfs/data/yanailab/projects/jw7078/processed_data/399-A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_IMAGING_CS/ALIGN_FIDUCIALS/fork0/chnk0-ue5873dae0f/files/fiducial_positions_list.txt",
    barcode_whitelist        = "visium-v1",
)
