resegment

Reprocess G4X-data with a new segmentation

Takes new cell-labels from a custom segmentation output and re-assigns transcripts
and protein signals to those cells. The operation recreates single-cell outputs and initializes a new G4X-viewer zarr store. Does not regenerate metrics.

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Usage

Arguments / Options

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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

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--cell-labels [required]

type : file path
example : path/to/segmentation.npz

Path to a new segmentation mask file containing cell labels. It will be used to create new single-cell outputs by aggregating transcript and protein data on those labels. The extent of the labels must match the shape of the original data.
Supported formats are: (.npy, .npz, .geojson)

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--labels-key

type : string
example : cell_id

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.

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--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.

--branch / -b

type : string
default : command name

Selects the processed-data branch used for command output. By default, some commands i.e redemux write to a command-specific branch: <G4X-DATA>/g4x-helpers/<command>.

Use a custom branch name to write to <G4X-DATA>/g4x-helpers/<branch>. This is useful when you want to keep multiple alternative outputs, or when you want to chain commands through the same branch.

g4x-helpers redemux G4X-DATA --branch custom_process ...
g4x-helpers resegment G4X-DATA --branch custom_process ...

Set --branch _src_ to write directly into the original G4X-DATA directory.

Warning

--branch _src_ edits the source data in place and may overwrite files produced by the command.

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