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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

Arguments / Options

G4X-DATA

type : directory
example : path/to/g4x_output

Positional path to a G4X sample output directory.
The folder must follow the expected schema (e.g., contain run_meta.json, segmentation masks, panel files, single-cell outputs).
Provide this argument directly after the specified command, i.e:
g4x-helpers COMMAND G4X-DATA

--in-place

type : flag
default : not set

By default, commands write their outputs to <G4X-DATA>/g4x_helpers/<command>, leaving the original data untouched. Using --in-place instead writes outputs directly into the specified G4X-DATA directory, which may be required when chaining certain commands.

Note: this will override any existing artifacts modified by the command.
Please refer to each feature’s documentation to see which files may be updated.



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