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"
input_channels: 3
output_channels: 5
CytosolSegmentationCellpose:
    input_channels: 2
    output_masks: 2
    shard_size: 120000000 # maxmimum number of pixel per tile
    overlap_px: 100
    nGPUs: 1
    chunk_size: 50 # chunk size for chunked HDF5 storage. is needed for correct caching and high performance reading. should be left at 50.
    threads: 1 # number of shards / tiles segmented at the same size. should be adapted to the maximum amount allowed by memory.
    cache: "."
    lower_quantile_normalization:   0.001
    upper_quantile_normalization:   0.999
    median_filter_size: 6 # Size in pixels
    nucleus_segmentation:
        model: "nuclei"
    cytosol_segmentation:
        model: "cyto2"
    chunk_size: 50
    filtering_threshold: 0.95
HDF5CellExtraction:
    compression: True
    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: "."
    hdf5_rdcc_nbytes: 5242880000 # 5gb 1024 * 1024 * 5000
    hdf5_rdcc_w0: 1
    hdf5_rdcc_nslots: 50000
CellFeaturizer:
    channel_classification: 4
    batch_size: 900
    dataloader_worker: 0 #needs to be 0 if using cpu
    inference_device: "cpu"
    screen_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