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OSS-Lite Server

OSS-Lite (OpenSlide Server-Lite) is a lightweight python web service that implements the IIIF Image API 2.1 specifications, and is built using the excellent digital pathology library called OpenSlide.

Usage

Getting started

Place all the images that are to be exposed to the API in a base folder. Let's call it /data/myImages/ for this example. The images could be organized in subfolders. E.g. /data/myImages/imageDir1, /data/myImages/imageDir2. The image files could be organized in the folders as: /data/myImages/imageDir1/image1.svs /data/myImages/imageDir1/image2.svs /data/myImages/imageDir2/image3.svs

Having set up the images and deploying oss-lite using deployment instructions, the service could be accessed using the following API calls.

Image Request API

Basic API syntax: {scheme}://{server}{/filepath}/{filename_with_extension}/{region}/{size}/{rotation}/{quality}.{format}

Example: http://localhost/data/myImages/imageDir2/image1.svs/8000,9000,400,400/full/0/default.jpg This returns a 400x400 tile starting at the left corner <8000,9000>, in JPEG format, from an image with filename image1.svs that is placed at /data/myImages on the host machine. To learn more about image request parameters visit IIIF Image API 2.1 webpage.

Image Information API

API syntax: {scheme}://{server}{/filepath}/{filename_with_extension}/info.json Example: http://localhost/data/myImages/imageDir2/image1.svs/info.json

Docker Container Deployment

Here we assume that all the images are in the base folder /data/myImages on the host machine and oss-lite will be deployed in a container and accessible at http://localhost/image-service To deploy oss-lite in a docker container, follow the following steps:

  • Clone this repo
  • cd oss-lite
  • docker build -t oss-lite .
  • docker run -itd -p <host_port>:5000 -v /data/myImages:/data/myImages oss-lite

This resulting docker container uses run.sh to start oss-lite as a daemon.

While deploying it along with Camicroscope Distro. Find out $CAMIC_IMAGES_DIR (How?), it is the directory on the host machine where all the images are stored by the image loader. Image loader will load images with path /data/images.

docker run -itd -p <host_port>:5000 -v $CAMIC_IMAGES_DIR:/data/images oss-lite

Deploying without Docker

To deploy oss-lite without Docker, follow the following steps:

  • Install openslide-tools and python-openslide
    On Ubuntu: sudo apt-get install openslide-tools python-openslide
  • Install python packages flask and gunicorn
    Using pip: pip install flask gunicorn
  • Clone this repo
  • cd oss-lite
  • gunicorn ossliteserver:app -w <num_threads> --bind 0.0.0.0:5000