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migrate

Upgrade legacy G4X-data layouts

Migrates legacy G4X-data into the current G4X-data schema used by G4X-helpers and G4X-viewer. The command copies and converts supported raw data and metadata into a new output directory, then optionally runs downstream processing to create single-cell output and a g4x-viewer.zarr compatible with G4X-viewer v4.

Usage

g4x-helpers migrate --help

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 sample.g4x, segmentation masks, panel files, images).
Provide this argument directly after the specified command, i.e:
g4x-helpers COMMAND G4X-DATA

--out-dir / -o [required]

type : directory
example : path/to/migrated_sample

Output directory for migrated data. The directory must already exist and must not already contain a sample.g4x file.

--check / -c

type : flag
default : not set

Check whether the legacy input can be migrated. This reports migration status without copying or converting data.

--roi

type : four integers
example : --roi 0 0 4096 4096

Restrict migration to a rectangular region of interest. Coordinates are provided as x0 y0 x1 y1 in pixel coordinates.

--no-downstream

type : flag
default : not set

Runs only the primary reprocessing step for the command and skips downstream single-cell processing and g4x-viewer.zarr generation.

Use this option when you want to inspect intermediate outputs or chain multiple processing steps before regenerating final single-cell and viewer outputs.

Examples

Check whether a legacy output can be migrated:

g4x-helpers migrate /path/to/legacy_sample \
    --out-dir /path/to/migrated_sample \
    --check

Migrate a full legacy output and generate downstream outputs:

g4x-helpers migrate /path/to/legacy_sample \
    --out-dir /path/to/migrated_sample

Migrate only raw data and metadata:

g4x-helpers migrate /path/to/legacy_sample \
    --out-dir /path/to/migrated_sample \
    --no-downstream

Migrate a region of interest:

g4x-helpers migrate /path/to/legacy_sample \
    --out-dir /path/to/migrated_sample \
    --roi 0 0 4096 4096



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