Repository Index

StarDist - Object Detection with Star-convex Shapes

• bioimage-analysis
• cell-segmentation
• nuclei-segmentation
• object-detection

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

• histopathology-images
• microscopy
• sliding-windows
• medical-image-analysis

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

Image quality is an open source software library for Image Quality Assessment (IQA).

• artificial-intelligence
• machine-learning
• image-quality-assessment
• computer-vision

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

• cellprofiler-analyst
• cellprofiler
• image-analysis
• machine-learning

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy

• biology
• fluorescence
• image-analysis
• image-processing

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology

HistoClean is a tool for the preprocessing and augmentation of images used in deep learning models. This easy to use application brings together the most popular image processing packages from across the python universe, meaning no more looking at documentation! HistoClean provides real time feedback to augmentations and preprocessing options. This allows users to evaluate their steps before implementation.

• image-processing
• images
• image-analysis
• deep-learning