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"
CytosolSegmentationCellpose:
    cache: "."
    nucleus_segmentation:
        model: "nuclei"
    cytosol_segmentation:
        model: "cyto2"
HDF5CellExtraction:
    threads: 80 # threads used in multithreading
    image_size: 400 # image size in pixel
    normalization_range: None #turn of percentile normalization for cells -> otherwise normalise out differences for the alexa647 channel
    cache: "."
CellFeaturizer:
    channel_selection: 4
    batch_size: 900
    dataloader_worker_number: 0 #needs to be 0 if using cpu
    inference_device: "cpu"
    label: "Ch3_Featurization"
LMDSelection:
    processes: 20
    segmentation_channel: 0
    shape_dilation: 16
    smoothing_filter_size: 25
    poly_compression_factor: 30
    path_optimization: "hilbert"
    greedy_k: 15
    hilbert_p: 7