3D Digital Pathology Visualization



Context

Histology, a subfield of pathology, deals with the medical analysis at microscopic level of tissue specimen from the human body. It is a cornerstone in health care and medical research. Digitization of the microscopy images opens new exciting possibilities. This includes moving from 2D image analysis to studying 3D structures and correlating them with in vivo imaging of the same tissue from CT or MR-imaging.

This Project

In this project tissue samples are studied on a scale of the cellular level. The aim of the project to develop efficient multi-scale visualizations of 3D stacks of collections of large-scale histology image. The colored images obtained by scanning of such tissue samples can exceed resolutions of 100,000 by 100,000 pixels at an optical magnification of 40x (>100 GiB per sample). The biggest challenges targeted include: The size of the datasets using volume rendering techniques; The design of effective transfer functions for RGB data in digital pathology; The development and evaluation of intuitive interfaces for the use by domain experts.
Digital Pathology Project website

Setting

The project builds upon a tight collaboration between computer scientists, pathologists, and clinical personnel.


Contact


Martin Falk, martin.falk at liu.se, website


People Involved


Funding


Collaborations


Publications

Posters


Martin Falk, Darren Treanor, Derek Magee, Claes Lundström: 3D Histology—Interactive High-resolution Volume Rendering for Pathology. Nordic Symposium on Digital Pathology, Linköping, Sweden, 2015.
[PDF], [Website]






Papers

Publications in 2017
Martin Falk, Ingrid Hotz, Patric Ljung, Darren Treanor, Anders Ynnerman, Claes Lundström
IEEE Pacific Visualization Symposium (PacificVis 2017) - 2017


Visualizations

3D histology inside the Inviwo framework

3D histology inside the Inviwo framework

3D slide stack of liver cirrhosis

3D slide stack of liver cirrhosis

3D slide stack of a colorectal polyp

3D slide stack of a colorectal polyp

3D slide stack of a colorectal polyp – close-up

3D slide stack of a colorectal polyp – close-up

3D slide stack of a colorectal polyp – close-up

3D slide stack of a colorectal polyp – close-up



Additional Resources