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


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


First clone the repo

git clone

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


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


To access the API in your browser


Example 1: to get list of all unique slide collections

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