`--update_bin`

Update G4X-Viewer `.bin` file with new metadata

Updates an existing .bin segmentation file with new clustering, embedding, or color metadata from a CSV file.

usage

$ update_bin 
  --bin_file /path/to/sample.bin
  --out_path /path/to/updated_sample.bin
  --metadata /path/to/metadata.csv

  # ─── optional ───
  --cellid_key <cellid_key>
  --cluster_key <cluster_key>
  --cluster_color_key <cluster_color_key>
  --emb_key <emb_key>
  --verbose <level>

argument descriptions

required

`--bin_file`: (type: `str`)

Path to the existing .bin file used by the G4X-Viewer. This file will be updated with metadata from the provided CSV file.

`--out_path`: (type: `str`)

Output path where the updated .bin file will be saved. The directory will be created if it doesn't already exist.

`--metadata`: (type: `str`)

Path to a CSV file containing metadata to update the .bin file. This file must include a header row and should contain cell IDs, optional cluster assignments, colors, and embeddings.

optional

`--cellid_key`: (type: `str` default: `None`)

Name of the column in the metadata file that contains cell IDs matching those in the .bin file. If not provided, the first column in the metadata will be used.

`--cluster_key`: (type: `str` default: `None`)

Column name in the metadata that provides cluster assignments for each cell. Required if --cluster_color_key is used.

`--cluster_color_key`: (type: `str` default: `None`)

Column name in the metadata that provides RGB or hex colors for each cluster. Must be used in conjunction with --cluster_key.

`--emb_key`: (type: `str` default: `None`)

Prefix for embedding coordinates. The script will look for two columns: {emb_key}_0 and {emb_key}_1. Used to embed cells in UMAP/tSNE/etc. space.

`--verbose`: (type: `int` default: `1`)

Logging verbosity level: - 0 = WARNING
- 1 = INFO
- 2 = DEBUG This affects how much information is printed to the console during execution.