This is a development workspace for a pathology viewer for the ADRC @ Emory using the DSA CodeBase
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README.md

README.md

ADRCPathViewer

This is a development workspace for a pathology viewer for the ADRC @ Emory using the DSA CodeBase. The repo contains two parts. The web service which used Python Flask-Restful and OpenSlide to serve whole-slide images, serve static pages and endpoints to the database.

Prerequisites

The following packages are required to run the API

  • OpenSlide and its dependencies (follow the instruction in this link)
  • openslide-python
  • flask_restful
  • flask_cache
  • bson
  • collections
  • threading
  • ConfigParser
  • pymongo

Installation

First clone the repo

git clone https://github.com/dgutman/ADRCPathViewer.git

Setup the client side (static HTML pages)

cd [APP_ROOT_DIR]/static

Run bower to install web app dependices

bower install

Run the API using the instructions below

Instuctions

To start the API execute the following command (run.py is located in the application root directory)

 ./run.py

To access the API in your browser

http://[yourdomain]:[port]/[version]/[resource]/[params]

Example 1: to get list of all unique slide collections

http://yourdomain.com:5000/v1/slidesetlist

Ecample 2: to get list of slides for one collection (BRCA)

http://yourdomain.com:5000/v1/slideset/BRCA

Application configurations

You make changes to the application configurations in app.cfg, some of the settings you can change are:

db_host: localhost (default)

db_port: 27017 (default)

db_name: your mongodb collection name

ws_host: 0.0.0.0 (default web service address)

ws_port: web service port

static_dir: location of static pages relative to the directory where the blueprint is located or an absolute path

slides_dir: location of the whole-slide images

tile_size: 256 (default)

overlap: 1 (default)

limit_bounds: 0 (default)

slide_cache_size: 1000 (default)

deepzoom_format: jpeg (default)