Image Translation for Multiplexed Whole Slide Images

A multiplexed image consists of multiple rounds of imaging. Each round has a DAPI frame along with several antigen frames. Frames in each round are assumed to be registered, but across rounds the frames may have been translated during imaging.

Rounds are identified by the integer ROUND_ID in each filename, separated by dot '.', prior to file type and marker. For example, the following filename

  UNMCPC.LIV.3rf77.1.DAPI.tif

Round ID = 1, Marker = DAPI, Type = tif

The script reg_multiplex_wsi.py translates all DAPI frames across all rounds. The DAPI frame of a random round is fixed and all other rounds with DAPI frames are translated with respect to this round. Corresponding translation vectors are applied to the rest of the antigen frames in each round.

All frames are expected in TIF format (with tif extension). Input frames are read from in_folder and output is written to out_folder. Inconsistent frame sizes are handled by 0-padding all frames to the larges frame size. Multichannel RGB frames are converted to grayscale frames prior to registration. A log file contains displacement estimates between each rounds. Larger displacement values may indicate unsuccessful translation for those rounds.

🚢 Docker

To generate a docker image:

1. Move the following files to a folder:

• Dockerfile
• unmc.yml
• register_multiplex_wsi.py

2. Build the docker image in that folder:

docker image build --tag mul_reg_wsi .

3. Point to input/ and output/ folders and run the container:

docker container run --rm --detach \
  --volume /path/to/output:/usr/src/app/output \
  --volume /path/to/input:/usr/src/app/input \
  --name register mul_reg_wsi

👥 Contributing

Within the Informatics Center, we value the health of our community as much as we do code. As a result, we ask you read through the following:

• Our contributor's guide tells what kinds of contributions we take.
• Our code of conduct delineates the standards of behavior we both practice and expect by everyone who participates with this software.

🔢 Versioning

We use the SemVer philosophy for versioning this software.

📃 License

The project is licensed under the Apache version 2 license.