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LIF Plate

Converts a Leica LIF file containing a multi-well plate acquisition into an OME-Zarr HCS plate.

Expected File Structure

The converter expects a .lif file where plate wells are organized under a named tile scan. Three plate layouts are supported:

One image per well, using flat well names (A1) or hierarchical well names (A/1):

Project.lif
└── Tilescan 1/
    ├── A1  (Simple Image)
    ├── B1  (Simple Image)
    └── ...

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

Multiple positions per well, named R1, R2, etc.:

Project.lif
└── Tilescan 1/
    ├── A1/
    │   ├── R1  (Simple Image)
    │   ├── R2  (Simple Image)
    │   └── ...
    └── ...

Project.lif
└── Tilescan 1/
    └── A/
        └── 1/
            ├── R1  (Simple Image)
            ├── R2  (Simple Image)
            └── ...

One mosaic (tiled) image per well:

Project.lif
└── Tilescan 1/
    ├── A1  (Mosaic Image)
    ├── B1  (Mosaic Image)
    └── ...

Project.lif
└── Tilescan 1/
    └── A/
        ├── 1  (Mosaic Image)
        └── ...

Names in curly braces (e.g., Tilescan 1) can be freely chosen. All other names must follow the conventions below.

Naming Conventions

Well names must be one or two letters followed by a positive integer:

  • Valid: A1, B2, AA1, AA12
  • Or hierarchical: A/1, A/2, AA/1

Position names (multi-position wells) must be R followed by a positive integer:

  • Valid: R1, R2, R12

Complex plate formats

If the LIF file contains additional sub-images (e.g., FLIM intensity maps), the converter ignores any entries that do not match the expected naming formats:

Project.lif
└── Tilescan 1/
    └── A/
        └── 1/
            ├── R1          ← converted
            └── R1/
                └── FLIM/
                    ├── Intensity      ← ignored
                    └── Fast Flim      ← ignored

Metadata

The converter extracts the following from the LIF file:

  • Well position (row and column)
  • Field-of-view index 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 tile scan to convert. If null, all tile scans in the file are converted (wildcard mode).
Plate Name str or null null Custom name for the output OME-Zarr plate. Defaults to the LIF file name.
Acquisition Id int 0 Acquisition identifier for combining multiple acquisitions into a single plate.
Advanced LifAcquisitionOptions {} Advanced options: condition table, 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_plate, LifPlateAcquisitionModel

acquisitions = [
    LifPlateAcquisitionModel(
        path="/path/to/plate.lif",
        plate_name="my_plate",
        acquisition_id=0,
    )
]

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

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