This is the official implementation for: a cross-platform informatics system for the Gut Cell Atlas: integrating clinical, anatomical and histological data.
Source code repository
https://github.com/MASILab/BarcodeRedcapIntegration
Get our docker image
To do
Run Code
(1) Run PrinterApp.py to print the barcode label.
(2) Run locationApp.py to do the data entry.
Description
The Gut Cell Atlas (GCA), an initiative funded by the Helmsley Charitable Trust, seeks to create a reference platform to understand the human gut, with a specific focus on Crohn’s disease. Although a primary focus of the GCA is on focusing on single-cell profiling, we seek to provide a framework to integrate other analyses on multi-modality data such as electronic health record data, radiological images, and histology tissues/images. Herein, we use the research electronic data capture (REDCap) system as the central tool for a secure web application that supports protected health information (PHI) restricted access.
Our innovations focus on addressing the challenges with tracking all specimens and biopsies, validating manual data entry at scale, and sharing organizational data across the group. We present a scalable, cross-platform barcode printing/record system that integrates with REDCap. The central informatics infrastructure to support our design is a tuple table to track longitudinal data entry and sample tracking.
Reference
A cross-platform informatics system for the Gut Cell Atlas: integrating clinical, anatomical and histological data
Shunxing Bao, Sophie Chiron, Yucheng Tang, Cody N. Heiser, Austin N. Southard-Smith, Ho Hin Lee, Marisol A. Ramirez, Yuankai Huo, Mary K. Washington, Elizabeth A. Scoville, Joseph T. Roland, Qi Liu, Ken S. Lau, Keith T. Wilson, Lori A. Coburn, and Bennett A. Landman
SPIE Medical Imaging 2021