voxelkit preview¶

voxelkit preview <file> --output preview.png

Generates a 2D PNG slice from your file and saves it to disk. The centre slice is used by default. You can control the plane, axis, and slice index with flags.

Usage¶

voxelkit preview FILE --output OUTPUT [options]

Arguments¶

Argument	Description
`FILE`	Path to a supported file

Flags¶

Flag	Format	Description
`--output PATH`	All	Required. Output `.png` file path
`--plane PLANE`	NIfTI only	One of `axial`, `coronal`, `sagittal`. Defaults to `axial`
`--dataset PATH`	HDF5 only	Dataset path inside the file, e.g. `data/subject01/run1/bold`
`--array NAME`	`.npz` only	Array name inside the archive
`--axis INT`	HDF5 / NumPy / TIFF	Axis to slice along (0, 1, or 2). Required for 3D HDF5 datasets
`--slice INT`	All	Slice index. Defaults to the centre slice

Format-specific flags

--plane is NIfTI-only. --dataset is HDF5-only. --array is .npz-only. Passing the wrong flag for a format raises an error.

Examples¶

NIfTIHDF5NumPy .npyNumPy .npzTIFF

# centre axial slice (default)
voxelkit preview bold.nii.gz --output preview.png

# specific plane and slice
voxelkit preview bold.nii.gz --plane coronal --slice 20 --output coronal.png

# dataset_path and axis required for 3D datasets
voxelkit preview experiment.h5 \
  --dataset data/subject01/run1/bold \
  --axis 2 \
  --slice 10 \
  --output h5_preview.png

voxelkit preview volume.npy --axis 0 --slice 5 --output npy_preview.png

voxelkit preview data.npz --array X --axis 0 --output npz_preview.png

voxelkit preview zstack.tiff --axis 0 --slice 25 --output tiff_preview.png

Output¶

The PNG is written to the path given by --output. Parent directories are created automatically if they don't exist. The image is grayscale, normalised to 0–255.