StarDist - Object Detection with Star-convex Shapes
- bioimage-analysis
- cell-segmentation
- nuclei-segmentation
- object-detection
Repository Index
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TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.
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
Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk
- cancer-imaging-research
- radiomics
- radiomics-features
- machine-learning
AI-based pathology predicts origins for cancers of unknown primary - Nature
- histology
- pathology
- wsi-images
- histopathology
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
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
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