config.yaml

path_list: "input/path_list.csv"

model_channels: "rybg"
model_type: "mae_contrast_supcon_model"
update_model: False

# Output configuration
output_dir: "./output"  # Directory for all output files (required for new CSV format)
create_csv: True
save_attention_maps: False
output_format: "individual"  # "individual" (.npy files) or "combined" (.h5ad file)
embeddings_only: False

# Performance configuration
# Defaults are conservative so the tool runs on any laptop out of the box.
# For faster throughput on a workstation or GPU machine, see the tuning hints below.
gpu: -1           # -1 = CPU (works everywhere). Set to 0, 1, … to use a specific GPU.
batch_size: 1     # Images processed per forward pass. Increase (e.g. 32–256) when a GPU is available.
num_workers: 0    # DataLoader worker processes. 0 = single-threaded main process (safe on all OS).
                  # Increase (e.g. 4–8) together with prefetch_factor for GPU throughput.
prefetch_factor: 2  # Batches pre-loaded per worker. Only active when num_workers > 0.
async_saving: False  # Async file I/O — only effective with output_format: "individual".