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:
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
--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)
--labels-key
type : string
example : cell_id
Specifies the identifier for segmentation labels when loading mask data:
If using a
.npzfile:
Provide the name of the array within the archive that corresponds to the segmentation mask (required if multiple arrays are stored).If using a
.geojsonfile:
By default, cell labels are expected in a column namedlabel.
Use this argument to override and select a different column as the label source.
--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-placeinstead writes outputs directly into the specifiedG4X-DATAdirectory, 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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