Python package for image-based profiling
- cytominer
- microscopy
- morphological-profiling
- python
Repository Index
47,133 repositories indexed
25–48 of 49 · Most stars
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
Inner ear models for Python
- python
- cochlea
- inner-ear
- model
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
- ai4science
- llm
- multiagent-systems
- prompt-engineering
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
- biology
- fluorescence
- image-analysis
- image-processing
Cell-by-cell testing for production Jupyter notebooks in JupyterLab
PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
- deep-generative-model
- deep-learning
- single-cell-data-integration
- single-cell-multiomics
MicroPython driver for the HX711 load cell interface.
Autonomous multi-agent framework to optimize scientific software
- acceleration
- agentic-ai
- ai-agents
- bioinformatics
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
- bioimage-analysis
- cell-classification
- computer-vision
- digital-pathology
Multigrate: multiomic data integration for single-cell genomics
3D shape analysis using deep learning
- cancer-biology
- cell-biology
- deep-learning
- geometric-deep-learning
A versatile single-cell cross-modality translation method via dual-aligned variational autoencoders
An interactive tool for segmenting yeast cells using deep learning.
Single-cell fluorescence microscopy data analysis
- microscopy
- fluorescence-microscopy-imaging
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
- bioinformatics
- cell-type-deconvolution
- computational-biology
- deconvolution
A small async DNS client for MicroPython
- esp32
- micropython
- rpi-pico-w
- asyncio
scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection
A python package to analyze the matrix fiber orientation and intensity around cells in fiber matrices (as a proxy for cellular forces).
- imaging
- microscopy
- contractility
- collagen
🔬Python package for high-throughput single-cell imaging analysis.
- microscopy-image-analysis
- single-cell-analysis
Interpretable modeling of cellular responses to drug perturbations using cycle consistence learning
MicroPython driver for the CS1237 Load Cell Interface/ADC