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sbi is a Python package for simulation-based inference, designed to meet the needs of both researchers and practitioners. Whether you need fine-grained control or an easy-to-use interface, sbi has …
Bayesian Inference for Tooth Emergence Simulation (BITES) - parameter optimization software for a morphodynamic model of tooth development.
Version 2 of the minc-toolkit, uses tools based on ITK version 4.x
Composable transformations of Python+NumPy programs: differentiate, vectorize, JIT to GPU/TPU, and more
Turn your coding agents into research agents
aider is AI pair programming in your terminal
Get up and running with Kimi, GLM, MiniMax, DeepSeek, gpt-oss, Qwen, Gemma and other models.
reviewer3 is a command line tool that uses LLMs to give constructive feedback about scientific `.docx` manuscripts.
Turn any agent into a life science expert with NVIDIA BioNeMo skills.
Source code and examples for searching structures using RANGE
A project scaffold generator for bioinformatics analysis
vivarium-collective / vivatyssue
Forked from DamCB/tyssueAn epithelium simulation library
BioEngine is a distributed AI platform that brings the power of cloud computing to bioimage analysis.
Software that can generate photos from paintings, turn horses into zebras, perform style transfer, and more.
Implementation of "GANs for Biological Image Synthesis"
Napari plugin to ease manual correction of epithelial movie segmentation
A differentiable JAX-based framework for vertex modeling and inverse design of epithelial tissues
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24, MICCAI'26]
PhysiBoSS / PhysiBoSS
Forked from MathCancer/PhysiCellPhysiBoSS 2.0: a sustainable integration of stochastic Boolean and agent-based modelling frameworks
TrackMate is your buddy for your everyday tracking.
ngio is a Python library to streamline OME-Zarr image analysis workflows.
Reference implementation of the Graph Exchange File Format