fractal-lif-converters 0.4.0

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

Lif to OME-Zarr Converters

This repository contains the code to convert Lif files to OME-Zarr format.

Installation

To install the package, run the following command:

pip install fractal-lif-converters

Plate Conversion

The lif converters package provides a simple interface to convert lif files to OME-Zarr Plate format. The package provides a high-level function convert_lif_plate_to_omezarr that takes a list of LifInputModel objects as input and converts the lif files to OME-Zarr format.

Example Usage

• Simple Plate Conversion: convert a single lif scene to a OME-Zarr Plate

  from pathlib import Path
  
  from lif_converters.wrappers import 
  convert_lif_plate_to_omezarr
  
  from lif_converters import LifInputModel
  
  conversion_list = [
      LifInputModel(
          lif_file_path="path/to/your.lif",
          plate_name="plate_name",
          tile_scan_name="tile_scan_name",
      )
  ]
  
  convert_lif_plate_to_omezarr(
      zarr_dir="path/to/exports/", # Directory path where the OME-Zarr file will be saved
      conversion_list=conversion_list,
      num_levels=5, # Number of levels to be created in the OME-Zarr file
      coarsening_xy=2, # Coarsening factor for the xy dimensions
      overwrite=True,
      verbose=True,
  )
  

• Multiplexing Plate Conversion: Convert multiple lif scenes to a single OME-Zarr plate with multiple acquisitions

  from pathlib import Path
  
  from lif_converters.wrappers import 
  convert_lif_plate_to_omezarr
  
  from lif_converters import LifInputModel
  
  conversion_list = [
      LifInputModel(
          lif_file_path="path/to/your.lif",
          plate_name="plate_name",
          tile_scan_name="tile_scan_name",
          acquisition_id=0,
      ),
      LifInputModel(
          lif_file_path="path/to/your.lif", # Can be the same lif file or a different one
          plate_name="plate_name", # MUST BE THE SAME AS THE FIRST ONE
          tile_scan_name="tile_scan_name",
          acquisition_id=1, # MUST BE DIFFERENT FROM THE FIRST ONE
      )
  ]
  
  convert_lif_plate_to_omezarr(
      zarr_dir="path/to/exports/", # Directory path where the OME-Zarr file will be saved
      conversion_list=conversion_list,
      num_levels=5, # Number of levels to be created in the OME-Zarr file
      coarsening_xy=2, # Coarsening factor for the xy dimensions
      overwrite=True,
      verbose=True,
  )
  

• Wildcard Plate Conversion: if no tile_scan_name is provided, the converter will convert all tile scans in the lif file. In this case, no acquisition_id or plate_name can be provided.

  from pathlib import Path
  
  from lif_converters.wrappers import 
  convert_lif_plate_to_omezarr
  
  from lif_converters import LifInputModel
  
  conversion_list = [
      LifInputModel(
          lif_file_path="path/to/your.lif",
      )
  ]
  
  convert_lif_plate_to_omezarr(
      zarr_dir="path/to/exports/", # Directory path where the OME-Zarr file will be saved
      conversion_list=conversion_list,
      num_levels=5, # Number of levels to be created in the OME-Zarr file
      coarsening_xy=2, # Coarsening factor for the xy dimensions
      overwrite=True,
      verbose=True,
  )
  

Supported Lif File Plate Layouts

The following plate layout 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)
  ------------/...
  

• Mosaique 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.

While the othe names must follow the following format:

• The well name must be a singe or duble letter followed by a positive integer. Valid examples are A1, A2, B1, AA1, AA12 etc.

• Alternatively, the well can be hierarchically structured, for example A/1, A/2, B/1, AA/1, AA/12 etc.

• If the well is a multi-position well, the positions must be named R followed by a positive integer. Valid examples are R1, R2, R3, R12 etc.

• In case of more complex plate formats, for example FLIM data, the converter will ignore the data that does not follow the above formats. For example:

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

OME-Zarr Image Conversion

The lif converters package provides a simple interface to convert lif files to OME-Zarr Image format. The package provides a high-level function convert_lif_image_to_omezarr that takes a list of LifInputModel objects as input and converts each element in a OME-Zarr Image.

Example Image Conversion

• Simple Image Conversion: convert a single lif scene to a OME-Zarr Image

  from pathlib import Path
  
  from lif_converters.wrappers import 
  convert_lif_image_to_omezarr
  
  from lif_converters import LifInputModel
  
  conversion_list = [
      LifInputModel(
          lif_file_path="path/to/your.lif",
          zarr_name="output",
          tile_scan_name="tile_scan_name", # Optional
      ),
      LifInputModel(
          lif_file_path="path/to/your.lif", # Can be the same lif file or a different one
          zarr_name="output2", # MUST BE DIFFERENT FROM THE FIRST ONE
          tile_scan_name="tile_scan_name_2", # If given, the converter will only convert the given tile scan
      )
  ]
  
  convert_lif_image_to_omezarr(
      zarr_dir="path/to/exports/", # Directory path where the OME-Zarr file will be saved
      conversion_list=conversion_list,
      num_levels=5, # Number of levels to be created in the OME-Zarr file
      coarsening_xy=2, # Coarsening factor for the xy dimensions
      overwrite=True,
      verbose=True,
  )
  

• Wildcard Image Conversion: if no tile_scan_name is provided, the converter will convert all tile scans in the lif file. In this case, no zarr_name can be provided.

  from pathlib import Path
  
  from lif_converters.wrappers import 
  convert_lif_image_to_omezarr
  
  from lif_converters import LifInputModel
  
  conversion_list = [
      LifInputModel(
          lif_file_path="path/to/your.lif",
      ),
  ]
  
  convert_lif_image_to_omezarr(
      zarr_dir="path/to/exports/", # Directory path where the OME-Zarr file will be saved
      conversion_list=conversion_list,
      num_levels=5, # Number of levels to be created in the OME-Zarr file
      coarsening_xy=2, # Coarsening factor for the xy dimensions
      overwrite=True,
      verbose=True,
  )
  

Supported Lif File Images Layouts

The following image layout 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)
  --------/...
  

• Mosaique Image

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

The names in curly braces {} can be freely chosen by the user. While the othe names must follow the following format:

If the scene is a multi-position image, the positions must be named Position followed by a space and a positive integer. Valid examples are Position 1, Position 2, Position 3, Position 12 etc.

Moreover, if the lif file contains scans that do not follow the above formats, the converter will ignore them.