omeify

omeify is a Python package designed to streamline the conversion of various image files, such as TIFF files, into the OME-TIFF format. The generated OME-TIFF files are deidentified following the MITI standard. This package relies on two Java tools: bioformats2raw 0.6.1 and raw2ometiff 0.4.1.

Docker quickstart

$ docker pull vacation/omeify:latest
$ docker run --rm -v $(pwd):$(pwd) -u $(id -u):$(id -g) vacation/omeify:latest omeify -h
usage: omeify [-h] --type {qptiff_mif,qptiff_he} [--series SERIES]
              [--rename_channels_json RENAME_CHANNELS_JSON] [--omit_uuid]
              [--output_json OUTPUT_JSON] [--cache_directory CACHE_DIRECTORY]
              [--compression {LZW,JPEG,Uncompressed}] [-v] [--version]
              input output

omeify: Convert images into OME-TIFF format

positional arguments:
  input                 Input image file path
  output                Output OME-TIFF file path

options:
  -h, --help            show this help message and exit
  --type {qptiff_mif,qptiff_he}
                        Input image type (qptiff_mif: Akoya mIF qptiff,
                        qptiff_he: Akoya H&E qptiff) (default: None)
  --series SERIES       Series number (integer) (default: 0)
  --rename_channels_json RENAME_CHANNELS_JSON
                        JSON file that contains channel renaming dictionary
                        (default: None)
  --omit_uuid           Omit UUID in OME tag (default: False)
  --output_json OUTPUT_JSON
                        Output file for run info (default: None)
  --cache_directory CACHE_DIRECTORY
                        Path to a directory for storing temporary Zarr
                        directories. Defaults to the system temporary folder.
                        (default: None)
  --compression {LZW,JPEG,Uncompressed}
                        Compression type for output OME-TIFF file (LZW, JPEG)
                        (default: LZW)
  -v, --verbose         Enable verbose logging (default: False)
  --version             Display omeify and constituent programs versions
                        (default: False)

Dependencies

• bioformats2raw: A Java application that converts various image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification. This tool is used in conjunction with raw2ometiff to produce a Bio-Formats 5.9.x ("Faas") or Bio-Formats 6.x (true OME-TIFF) pyramid.
• raw2ometiff: A Java application that converts a directory of tiles to an OME-TIFF pyramid. This tool is the second half of the iSyntax/.mrxs to OME-TIFF conversion process.

Note: As omeify is licensed under the MIT license, the GPL-licensed dependencies (bioformats2raw and raw2ometiff) are not included. Instructions on how to install these dependencies will be provided later.

MITI Standard

omeify follows the Minimum Information guidelines for highly multiplexed tissue images (MITI) to ensure the highest standards in data and metadata handling. The MITI standard is specifically designed for tissue atlases that combine multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens. This standard guides data deposition, curation, and release.

Installation

1. Install the omeify package:

pip install omeify

Usage

Command Line Interface (CLI)

You can use omeify through the command line interface by running the following command:

$ omeify -h
usage: omeify [-h] --type {qptiff_mif,qptiff_he} [--series SERIES]
              [--rename_channels_json RENAME_CHANNELS_JSON] [--omit_uuid] [--output_json OUTPUT_JSON]
              [--cache_directory CACHE_DIRECTORY] [--compression {LZW,JPEG,Uncompressed}] [-v]
              [--version]
              input output

omeify: Convert images into OME-TIFF format

positional arguments:
  input                 Input image file path
  output                Output OME-TIFF file path

options:
  -h, --help            show this help message and exit
  --type {qptiff_mif,qptiff_he}
                        Input image type (qptiff_mif: Akoya mIF qptiff, qptiff_he: Akoya H&E qptiff)
                        (default: None)
  --series SERIES       Series number (integer) (default: 0)
  --rename_channels_json RENAME_CHANNELS_JSON
                        JSON file that contains channel renaming dictionary (default: None)
  --omit_uuid           Omit UUID in OME tag (default: False)
  --output_json OUTPUT_JSON
                        Output file for run info (default: None)
  --cache_directory CACHE_DIRECTORY
                        Path to a directory for storing temporary Zarr directories. Defaults to the
                        system temporary folder. (default: None)
  --compression {LZW,JPEG,Uncompressed}
                        Compression type for output OME-TIFF file (LZW, JPEG) (default: LZW)
  -v, --verbose         Enable verbose logging (default: False)
  --version             Display omeify and constituent programs versions (default: False)

Python API

You can also use omeify within your Python scripts:

from omeify.inputs import AkoyaMIFQptiff, AkoyaHEQptiff

input_processor = AkoyaMIFQptiff(input_file_path, series=series_number)
input_processor.rename_channels = rename_channels_dict

output_info = input_processor.convert(output_file_path, display_uuid=True)

Replace AkoyaMIFQptiff with AkoyaHEQptiff if you are working with H&E qptiff files.

License

This project is licensed under the MIT License. Please note that the bioformats2raw and raw2ometiff dependencies are licensed under the GPL License and are not included in this repository.