Digital Pathology Resources

The Penn Digital Pathology Lab believes in open source tools and the sharing of digital pathology resources to increase the rigor and reproducibility of our methods. We include links below to open-source software we utilize in our lab:

• QuPath 0.2.0-m5 
• GitHub 
• ImageJ

Including software tools developed by our friends and colleagues at PICSL

• Histolozee
• ITK-SNAP

COMING SOON

Downloadable custom scripts for human brain histology sampling and analysis in QuPath along with video tutorials (please check back with us soon).

Published Methods Papers

• Irwin David J, Byrne Matthew D, McMillan Corey T, Cooper Felicia, Arnold Steven E, Lee Edward B, Van Deerlin Vivianna M, Xie Sharon X, Lee Virginia M-Y, Grossman Murray, Trojanowski John Q: Semi-Automated Digital Image Analysis of Pick's Disease and TDP-43 Proteinopathy. The journal of histochemistry and cytochemistry: official journal of the Histochemistry Society 64(1): 54-66, Jan 2016.

• Giannini Lucia A A, Xie Sharon X, Peterson Claire, Zhou Cecilia, Lee Edward B, Wolk David A, Grossman Murray, Trojanowski John Q, McMillan Corey T, Irwin David J*: Empiric Methods to Account for Pre-analytical Variability in Digital Histopathology in Frontotemporal Lobar Degeneration. Frontiers in neuroscience 13: 682, 2019 Notes: *Corresponding Author.