HistomicsUI

Organize, visualize, and analyze histology images.

HistomicsUI organizes and managed whole slide image (WSI) files using Girder. It has a dedicated interface to select WSI, add annotations manually, and to run analysis and algorithms on all or parts of images.

Girder provides authentication, access control, and diverse storage options, including using local file systems and Amazon S2. WSI images are read and displayed via the large_image module. Algorithms are containerized using Docker and are run using the slicer_cli_web Girder plugin. These can be run on multiple worker machines via Girder Worker and celery.

A set of common algorithms are provided by HistomicsTK.

Installation

Linux

In linux with Python 2.7, Python 3.5, 3.6, or 3.7:

Prerequisites:

• MongoDB must be installed and running.
• An appropriate version of Python must be installed.

pip install histomicsui --find-links https://girder.github.io/large_image_wheels
girder build
girder serve

To use Girder Worker:

pip install girder_slicer_cli_web[worker]
GW_DIRECT_PATHS=true girder_worker -l info -Ofair --prefetch-multiplier=1

The first time you start HistomicsUI, you'll also need to configure Girder with at least one user and one assetstore (see the Girder documentation). Additionally, it is recommended that you install the HistomicsTK algorithms. This can be done going to the Admin Console, Plugins, Slicer CLI Web settings. Set a default task upload folder, then import the dsarchive/histomicstk:latest docker image.

Reference Deployment

The standard deployment of HistomicsUI is the Digital Slide Archive. The associated repository has tools for readily installing via Docker, VirtualBox, or shell scripts on Ubuntu.

Funding

This work is funded in part by the NIH grant U24-CA194362-01.