camicroscope/oss-lite2 repository overview

⁠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