resegment

Reprocess G4X-output with a new segmentation

Replaces or updates the segmentation mask in a G4X run and regenerates all downstream single-cell data and .bin files.

Usage

Note

Global options --threads/-t & --verbose/-v must be supplied on the main entrypoint before the subcommand:

g4x-helpers --threads 16 -v 2 COMMAND /path/to/g4x_data [OPTIONS]

use g4x-helpers --help for more information

argument descriptions

---

required

G4X-DATA (argument)

Positional path to a G4X sample output directory.
The folder must follow the expected schema (e.g., run_meta.json, segmentation masks, panel files, single-cell outputs).
Provide this argument after command-specific options.

--cell-labels: (type: str)

Path to the new segmentation mask file. Supported formats include .npy, .npz, and .geojson. This file will be used to replace the existing mask for transcript and protein signal assignment.

optional

--labels-key: (type: str default: None)

Specifies the identifier for segmentation labels when loading mask data:

• If using a .npz file:
  Provide the name of the array within the archive that corresponds to the segmentation mask (required if multiple arrays are stored).

• If using a .geojson file:
  By default, cell labels are expected in a column named label.
  Use this argument to override and select a different column as the label source.

--in-place: (flag default: False)

By default, outputs are written to <G4X-DATA>/g4x_helpers/<command>, leaving the source data untouched.
Add --in-place to write results directly into the provided G4X-DATA folder (overwriting existing artifacts for that command).

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