`new_bin`

Generate G4X-viewer `.bin` files from G4X sample output

This tool will create a new .bin segmentation file compatible with the G4X-viewer using the processed output from a G4X run. This is typically only needed to update older outputs to newer versions of the .bin format.

Usage

g4x-helpers new_bin --help

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.

optional

`--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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