Repository Index

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

C library for reading virtual slide images

• pathology
• whole-slide-imaging
• c

Tools for computational pathology

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

[Deprecated] This project can make it easy to theme and custom Android's dialog. Also provides Holo and Material themes for old devices.

• android
• dialog
• material-theme

Code and data used to create the examples in "Evidence-based Software Engineering based on the publicly available data"

• cognitive-capitalism
• cognitive-science
• economic-models
• ecosystem-modeling

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

• ai
• cell
• digitalpathology
• microscopy

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI (Nature Medicine). PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

• artificial-intelligence
• clip
• pathology
• vision-and-language

Strategy game based on history, mythology and fiction

Fusing Histology and Genomics via Deep Learning - IEEE TMI

• pathomic
• fusion
• multimodal
• pathology

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

• histology
• pathology
• wsi-images
• histopathology

Interoperable web-based DICOM slide microscopy viewer and annotation tool

• dicomweb
• oidc
• react
• digital-pathology

⚡ Open-source software for deep learning-based digital pathology

• deep-learning
• machine-learning
• digital-pathology
• computational-pathology

Python package for image-based profiling

• cytominer
• microscopy
• morphological-profiling
• python

Collection of mathematical morphology methods and plugins for ImageJ

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

Describe a thing, get a hologram, a 3D model and its parts: built by any AI agent, honestly.

• 3d-visualization
• agent-skills
• ai-agents
• claude-code

Translated麦门双预算军师 (Maimen Dual-Budget Strategist) · McDonald's China MCP contest entry | Dual-budget (money + calories) McDonald's China MCP Agent Skill with 3-tier meal plans, coupon math and a holographic persona card. One budget for money and one for calories; a meal is only put together when it passes both gates at once: 88,788 combinations are exhaustively searched locally, giving best-value / most substantial / most balanced tiers and the price after coupons.

• agent-skills
• ai-agent
• budget
• budgeting

An NLP library for Uralic languages such as Finnish, Skolt Sami, Moksha and so on. Also supporting some non-Uralic languages such as Spanish, French, Arabic, Swedish, Norwegian, Russian and English. LLMs, FSTs and More!

• nlp-library
• uralic-languages
• finnish
• sami

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

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

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

• r
• neuroanatomy-toolbox
• cran
• neuron

The Harmony Python library: a research tool for psychologists to harmonise data and questionnaire items. Open source.

• data-harmonization
• data-science
• depression
• harmonisation

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting

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

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