QuPath - Open-source bioimage analysis for research

groovy opencv machine-learning imagej javafx image-processing histology cell-segmentation bioimage-informatics digital-pathology pathology whole-slide-imaging cell-analysis computational-pathology bioimage-analysis tissue-microarray-analysis

• Updated Nov 11, 2026
• Java

Code for our BVM workshop submission "Attention-based Multiple Instance Learning for Survival Prediction on Lung Cancer Tissue Microarrays"

deep-learning lung-cancer computational-pathology tissue-microarray-analysis multiple-instance-learning histopathology

• Updated Dec 16, 2022
• Jupyter Notebook

Tissue Microarray Auto De-Array

medical-imaging pathology tissue-microarray-analysis

• Updated Apr 28, 2022
• Python

Perform RESTORE normalization on multiplexed imaging data.

normalization tissue-microarray-analysis multiplexed-imaging spatial-omics

• Updated Jun 22, 2023
• Python

batchtma: R package to adjust for batch effects, for example between tissue microarrays

measurement-error batch-effects tissue-microarray-analysis

• Updated Oct 10, 2026
• R