StarDist - Object Detection with Star-convex Shapes
- bioimage-analysis
- cell-segmentation
- nuclei-segmentation
- object-detection
Repository Index
47,133 repositories indexed
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Plant phenotyping with image analysis
- science
- bioinformatics
- image-analysis
- plant-phenotyping
An elegant Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
- itk
- insight-toolkit
- jupyter
- jupyter-widget
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
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
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
Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
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
Tool for segmentation in bioimaging
- napari
- bioimage-analysis
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
Lattice light-sheet post-processing utility.
- microscopy
- light-sheet
- image-processing
- image-analysis
🔬Python package for high-throughput single-cell imaging analysis.
- microscopy-image-analysis
- single-cell-analysis