Automated laboratory diagnostics

Although microscopes are common in Uganda and other developing countries, a shortage of lab technicians to operate them means that access to quality diagnostic services is limited for much of the population. This leads to misdiagnoses of disease, which in turn causes life-threatening conditions to be incorrectly treated, drug resistance, and the economic burden of buying unecessary drugs. Even where health facilities have lab technicians, they are often oversubscribed and have difficulty spending enough time on each sample to give a confident diagnosis.

Given that smartphones are widely owned across the developing world, there is a technological opportunity to address this problem: phones can be used to capture and process microscopy images. This project aims to produce a functioning point-of-care diagnosis system on this principle, capable of running on multiple microscope and phone combinations. Our work exploits recent technological advances in 3D printing and deep learning to produce effective hardware and software respectively. The diagnostic challenges being focussed on are malaria (in blood samples), tuberculosis (in sputum samples) and intestinal parasites (in stool samples).

Hardware

Additive manufacturing, or 3D printing, provides an opportunity to create one-off customised adapters for any cameraphone and microscope combination, as long as we know the geometry of each. It also dramatically reduces the development costs for new products, and allows rapid prototyping capabilities and easy repair. 3D shapefiles for printing the adapter

This hardware on its own has various applications beyond point-of-care diagnostics, including telemedicine, teaching, and the archival of images used for diagnosis (useful for later verification).

The sample images below were captured using our experimental setup:

Software

The software component of our work is to train machine learning methods to recognise different pathogen objects, and to test usability at the point of care. Deep learning methods for object detection have allowed us to improve the speed and accuracy of diagnosis compared to previous alternatives.

December 2016

Complete files accompanying the convolutional networks paper are now available online, including annotated images captured using the smartphone adapter setup shown above, hardware specifications and source code.

• Annotated malaria image dataset (118 MB): 1182 thick blood smear images with bounding boxes of 7245 parasites.
• Annotated tuberculosis image dataset (456 MB): 928 sputum images with bounding boxes of 3734 bacilli.
• Annotated intestinal parasites image dataset (438 MB): 1217 stool images with bounding boxes of 162 parasite eggs (hookworm, taenia and hymenolepsis nana).
• Source code for convolutional net training and evaluation
• 3D-printable smartphone microscope adapter shapefiles

If making use of these resources, please cite the paper below.

August 2016

Our paper in Machine Learning in Health Care extends the results on deep convolutional networks to tuberculosis and intestinal parasite detection, and using exclusively images captured by smartphone.

• J.A. Quinn, R. Nakasi, P.K. Mugagga, P. Byanyima, W. Lubega, A. Andama. Deep Convolutional Neural Networks for Microscopy-Based Point of Care Diagnostics. Proceedings of the International Conference on Machine Learning for Health Care, Journal of Machine Learning Research W&C track, Volume 56, 2016. pdf.

September 2015

Carlos Sánchez Sánchez, supervised by Chris Williams, has completed his MSc thesis on plasmodium detection, showing that Deep Convolutional Networks give significant accuracy increases for plasmodium detection over the previous methodology.

• C. Sánchez Sánchez. Deep Learning for Identifying Malaria Parasites in Images, MSc thesis, University of Edinburgh, 2015. pdf

December 2014

A complete reference system for malaria detection, with object detection based on morphological image features, can be downloaded:

• Annotated image dataset of plasmodium (malaria parasite), including 2703 images with bounding boxes of 50,255 parasites. Download images and annotation
• Reference system for parasite detection: Download source code

Please cite the following paper if making use of this code or data:

J.A. Quinn, A. Andama, I. Munabi, F.N. Kiwanuka. Automated Blood Smear Analysis for Mobile Malaria Diagnosis. Chapter in Mobile Point-of-Care Monitors and Diagnostic Device Design, eds. W. Karlen and K. Iniewski, CRC Press, 2014. pdf

Team

Core team:

• Alfred Andama, Principal Laboratory Technician
• David Byansi, Research Assistant (Data collection/annotation/archival)
• Ezra Rwakazooba, Research Assistant (Server development)
• John Quinn, Principal Investigator
• Kenan Pollack, 3D printing
• Patrick Byanyima, Laboratory Technician
• Pius Kavuma, Research Assistant (Hardware design/manufacture + mobile development)
• Rose Nakasi, Research Assistant (Computer vision)
• Vincent Wadda, Laboratory Technician
• William Lubega, Computer Science PGD researcher and medical doctor

External collaborators:

• Carlos Sánchez Sánchez, University of Edinburgh
• Chris Williams, University of Edinburgh
• Stathis Lempesis, University of Edinburgh
• Design Without Borders

Funded by Grand Challenges Canada, under the Stars in Global Health progam.