Algorithm that won 2nd place in the TIGER Challenge for breast cancer survival prediction by counting TILs.

NeMo Guardrails is an open-source toolkit for easily adding programmable guardrails to LLM-based conversational systems.

R toolkit for single cell genomics

Demo of a customer service use case implemented with the OpenAI Agents SDK

Scripts for data processing

DPool; Previously POPPSlide: Patient Outcome Prediction Pipeline using Whole Slide Images

Data analysis for manuscript "Artificial intelligence-based quantification of lymphocytes in feline small intestinal biopsies"

Files associated with the From Samples To Knowledge 2025 QuPath training course

Various scripts written for image analysis utilities

QuPath extension to interactively align images

The official QuPath extension for InstanSeg

QuPath extension to run StarDist nucleus detection

QuPath extension for Segment Anything Model (SAM)

PAthological QUpath Obsession - QuPath and Python conversations

Config files for my GitHub profile.

Convert Seurat objects to 10x Genomics Loupe files.

an extension that wraps a Cellpose environment such that WSI can be analyzed using Cellpose through QuPath.

3D Extension of the Cellpose Algorithm by Stringer et al., 2021.

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

QuPath - Open Source Digital Pathology