fractal-lif-converters 0.6.0

Converter from the Lif files (Leica Microscope) to OME-Zarr format.

Lif to OME-Zarr Converters

A collection of Fractal tasks to convert Leica .lif files into OME-Zarr format.

Tasks

Task	Use case
Convert Lif Plate to OME-Zarr	Convert a .lif containing a plate-shaped tile-scan into an OME-Zarr HCS plate.
Convert Lif Scene to OME-Zarr	Convert a single scene (single-position, multi-position, or mosaic) into a standalone OME-Zarr image.

Each task is a Fractal compound task: an init step parses the .lif metadata and builds the parallelization list, and a compute step writes the image data well-by-well (or scene-by-scene).

Installation

pip install fractal-lif-converters

Supported Lif File Plate Layouts

The following plate layouts are supported:

• Single Position Plates

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/A
  ------------/1 (Simple Image)
  

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/A1 (Simple Image)
  --------/...
  

• Multi Position Plates

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/A
  ------------/1
  ----------------/R1 (Simple Image)
  ----------------/R2 (Simple Image)
  ----------------/...
  

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/A1
  ------------/R1 (Simple Image)
  ------------/R2 (Simple Image)
  ------------/...
  

• Mosaic Plates

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/A
  ------------/1 (Mosaic Image)
  ------------/...
  

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/A1 (Mosaic Image)
  --------/...
  

The names in curly braces {} can be freely chosen by the user. The other names must follow these conventions:

• Well names are a single or double letter followed by a positive integer. Valid examples: A1, A2, B1, AA1, AA12.

• Wells can also be hierarchically structured, e.g. A/1, A/2, B/1, AA/1, AA/12.

• Multi-position wells use R followed by a positive integer for each position: R1, R2, R3, R12.

• For more complex layouts (e.g. FLIM), the converter ignores any data that doesn't follow the conventions above. For example:

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/A/1/R1 (Converted)
  --------/A/1/R1/FLIM/Intensity (Ignored)
  --------------------/Fast Flim (Ignored)
  --------------------/Standard Deviation (Ignored)
  

Supported Lif File Image Layouts

The following image layouts are supported:

• Single Position Image

  /{Project.lif}
  ----/{Tilescan 1} (Simple Image)
  

• Multi Position Image

  /{Project.lif}
  ----/{Tilescan 1}/
  --------/Position 1 (Simple Image)
  --------/Position 2 (Simple Image)
  --------/...
  

• Mosaic Image

  /{Project.lif}
  ----/{Tilescan 1} (Mosaic Image)
  

The names in curly braces {} can be freely chosen by the user. For multi-position images the position names must be Position followed by a space and a positive integer, e.g. Position 1, Position 2, Position 12. Scans that don't follow these conventions are ignored.