Repository Index

StarDist - Object Detection with Star-convex Shapes

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

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

• medical-imaging
• medical-ai
• deep-learning
• machine-learning

Plant phenotyping with image analysis

• science
• bioinformatics
• image-analysis
• plant-phenotyping

Segment Anything for Microscopy

• microscopy-images
• segment-anything
• segmentation
• cell-segmentation

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

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

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

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

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

• python
• microscopy
• scripting
• automation

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

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

Collection of mathematical morphology methods and plugins for ImageJ

• image-processing
• image-analysis
• imagej
• fiji

A curated list of awesome cytodata resources https://www.cytodata.org/awesome-cytodata/

• awesome-list
• awesome
• image-analysis
• morphology

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