Pyramidal-TIFF

Convert slides/images to pyramidal tiff

1. Docker environement

a. Build docker image from Dockerfile

$ docker build -t pyramidal_tiff:chen .

• or pull from Docker Hub

$ docker pull pingjunchen/pyramidal_tiff:chen
$ docker tag pingjunchen/pyramidal_tiff:chen pyramidal_tiff:chen

b. Run docker container

$ docker run -it --rm --user $(id -u):$(id -g) \
  -v ${CODE_ROOT}:/App/Pyramidal-TIFF \
  -v ${DATA_ROOT}:/Data \
  --shm-size=128G --cpuset-cpus=0-19 \
  --name pyramidal_tiff_chen pyramidal_tiff:chen

• For example:

$ docker run -it --rm --user $(id -u):$(id -g) \
  -v /rsrch1/ip/pchen6/Codes/CHEN/Pyramidal-TIFF:/App/Pyramidal-TIFF \
  -v /rsrch1/ip/pchen6/DataCollection/PyramidalTIFF:/Data \
  --shm-size=128G --cpuset-cpus=0-19 \
  --name pyramidal_tiff_chen pyramidal_tiff:chen

2. Pyramidal tiff conversion

• Convert slides

$ python convert_slide.py --raw_slide_dir RawSlides --raw_slide_suffix .svs

• Convert images

$ python convert_image.py --raw_img_dir RawImages --raw_img_suffix .tif