Config Files

The configuration file is a .yml file which specifies all of the parameters for each of the methods chosen in a specific scPortrait Project run.

Example Configuration File

---
name: "Cellpose Segmentation"
ShardedCytosolSegmentationCellpose:
    shard_size: 2000000 # maxmimum number of pixel per tile
    overlap_px: 100
    nGPUs: 1
    threads: 2 # number of shards / tiles segmented at the same size. should be adapted to the maximum amount allowed by memory.
    cache: "."
    nucleus_segmentation:
        model: "nuclei"
    cytosol_segmentation:
        model: "cyto2"
    match_masks: True
    filter_masks_size: False
HDF5CellExtraction:
    threads: 80 # threads used in multithreading
    image_size: 128 # image size in pixel
    normalize_output: True
    normalization_range: (0.01, 0.99)
    cache: "."
CellFeaturizer:
    batch_size: 900
    dataloader_worker_number: 10 #needs to be 0 if using cpu
    inference_device: "cpu"
LMDSelection:
    threads: 20
    cache: "."
    processes_cell_sets: 10
    # defines the channel used for generating cutting masks
    # segmentation.hdf5 => labels => segmentation_channel
    # When using WGA segmentation:
    #    0 corresponds to nuclear masks
    #    1 corresponds to cytosolic masks.
    segmentation_channel: "seg_all_nucleus"
    shape_dilation: 16
    smoothing_filter_size: 25
    rdp_epsilon: 0.6
    path_optimization: "hilbert"
    greedy_k: 15
    hilbert_p: 7