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LIF Image

Converts one or more images from a Leica LIF file into standalone OME-Zarr images (not a plate structure).

Expected File Structure

The converter expects a .lif file where each image to convert is a named entry at the top level or nested one level deep. Three image layouts are supported:

A single image directly under the scan name:

Project.lif
└── Tilescan 1  (Simple Image)

Multiple positions under a scan, named Position 1, Position 2, etc.:

Project.lif
└── Tilescan 1/
    ├── Position 1  (Simple Image)
    ├── Position 2  (Simple Image)
    └── ...

A single mosaic (tiled) image under the scan name:

Project.lif
└── Tilescan 1  (Mosaic Image)

Names in curly braces (e.g., Tilescan 1) can be freely chosen. Scans that do not match any of the supported layouts are ignored automatically.

Naming Conventions

Position names (multi-position images) must be Position followed by a space and a positive integer:

  • Valid: Position 1, Position 2, Position 12

Metadata

The converter extracts the following from the LIF file:

  • Image name and stage positions (X, Y, Z)
  • Channel names and IDs
  • Pixel size (XY and Z spacing in micrometers)
  • Timepoint indices
  • Mosaic tile layout (for mosaic images)

Task Parameters

Field Type Default Description
Path str required Path to the .lif file.
Tile Scan Name str or null null Name of the scan to convert. If null, all compatible scans in the file are converted (wildcard mode).
Zarr Name str or null null Custom name for the output OME-Zarr image. Defaults to the scan name.
Advanced LifAcquisitionOptions {} Advanced options: stage corrections, filters, and LIF-specific settings. See Converters Overview.

Limitations

  • This converter has been tested on a limited set of LIF acquisitions and may not handle all formats.
  • Images exported in Leica auto-saved mode are not supported.

Python API

from fractal_lif_converters import convert_lif_image, LifImageAcquisitionModel

acquisitions = [
    LifImageAcquisitionModel(
        path="/path/to/image.lif",
    )
]

convert_lif_image(
    zarr_dir="/output/zarr",
    acquisitions=acquisitions,
)

See How to Run the Converters for all common parameters and execution details.