Manipulation and analysis of geometric objects
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Mesa is an open-source Python library for agent-based modeling, ideal for simulating complex systems and exploring emergent behaviors.
- mesa
- agent-based-modeling
- agent-based-simulation
- simulation-framework
3D visualization and mesh analysis for science and engineering
- vtk
- python
- visualization
- 3d
POT : Python Optimal Transport
- optimal-transport
- numerical-optimization
- machine-learning
- emd
A python module for scientific analysis of 3D data based on VTK and Numpy
- 3d-graphics
- vtk
- 3d
- mesh
Deep probabilistic analysis of single-cell and spatial omics data
- scrna-seq
- variational-bayes
- variational-autoencoder
- cite-seq
Plant phenotyping with image analysis
- science
- bioinformatics
- image-analysis
- plant-phenotyping
An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
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
Main yt repository
- data
- visualization
- analysis
- python
skimpy is a light weight tool that provides summary statistics about variables in data frames within the console.
- eda
- pandas
- data-science
- exploratory-data-analysis
A Python native dynamical system simulation framework in the block diagram paradigm.
- blockdiagram
- control-systems
- hierarchical-modeling
- nonlinear-dynamics
cell detection in calcium imaging recordings
- imaging
- neuroscience
- data-analysis
Tools for computational pathology
- machine-learning
- digital-pathology
- computational-pathology
- biomedical-image-processing
Multiple Pairwise Comparisons (Post Hoc) Tests in Python
- posthoc-comparisons
- posthoc-tests
- python
- scikit
OPEM (Open Source PEM Fuel Cell Simulation Tool)
- chemistry
- pem
- fuel-cell
- opem
Automated 3D cell detection in very large images
- microscopy
- cell-detection
- deep-learning
- image-analysis
MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.
Easy link prediction tool
- python
- network-analysis
- link-prediction
- research
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
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
A fast MDCT implementation using SciPy and FFTs
- scientific-computing
- signal-processing
- scipy
- audio-analysis
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning