Microscopy
Showing 36 of 36 projects
A generalist algorithm for cellular segmentation with human-in-the-loop training and superhuman generalization across diverse microscopy images.
An open-source, N-dimensional image processing platform for scientific imaging with a modular, headless architecture.
An open-source application for automated biological image analysis, enabling biologists to measure phenotypes from thousands of images.
Public domain Java software for processing and analyzing scientific images across multiple platforms.
Interactive segmentation and tracking tools for microscopy images built on Segment Anything.
A free Google Colab-based toolbox with Jupyter notebooks and GUI for applying deep learning to microscopy data without coding expertise.
A sliding window framework for classifying high-resolution whole-slide microscopy and histopathology images using deep neural networks.
A C library for reading whole slide image files (virtual slides) with a consistent API across multiple vendor formats.
An open-source toolkit for scalable, standardized computational pathology analysis, enabling AI and machine learning on large imaging datasets.
A vision transformer-based deep learning model for automated instance segmentation and classification of cell nuclei in histopathology images.
An open and extensible Fiji plugin for single-particle tracking in life-science microscopy images.
A PyTorch-based Python package for deep and machine learning analysis of microscopy data, designed for domain scientists.
Automated 3D cell detection and classification in large-scale volumetric brain images using deep learning.
A Python library for reading, writing, and converting microscopy image formats with support for OME-TIFF, CZI, ND2, and more.
A foundation model for cell segmentation that achieves state-of-the-art performance across diverse cellular targets and imaging modalities.
A PyTorch-based segmentation toolbox for electron microscopy connectomics, enabling neural structure analysis in 3D volumes.
A curated list of software, tools, pipelines, and plugins for image analysis in biological research.
A Python API for downloading and processing neuroanatomical atlas data from multiple sources.
A curated directory of open-source projects, tools, and resources for microscopy research and development.
A Python library for serverless, random-access reading and writing of Neuroglancer Precomputed format volumes, meshes, and skeletons.
A collection of tools and scripts to automate microscopy workflows in ZEN Blue using Python, APIs, and AI tools.
A lightweight C/C++ library for fast reading and writing of basic multi-frame TIFF files.
Automated 3D brain image registration tool for aligning sample data with anatomical atlases across multiple species.
A Python package for processing and normalizing high-dimensional morphological feature data from high-throughput cell imaging experiments.
A deep learning tool for automatic axon and myelin segmentation from microscopy images using convolutional neural networks.
A Fiji plugin for pixel-based image segmentation using Weka machine learning algorithms and image features.
An automated pipeline for organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy.
R package for segmentation, registration, and web-based atlas generation from microscope brain images.
A Python package for simulating optical transfer functions and point spread functions of optical microscopes.
A machine learning framework for automated cell segmentation in bioimages using parametric spline curves.
A lightweight image viewer for non-experts to interactively explore complex multiplexed tissue images.
A Python package for applying Gaussian processes and Bayesian optimization to images and hyperspectral data using Pyro and Gpytorch.
An R package for processing and analyzing high-dimensional morphological profiling data from image-based cell biology.
Pure Python library for reading NIS Elements ND2 microscopy images and metadata using the pims framework.
A Python tool for stitching large volumetric images from light-sheet fluorescence microscopy.
A napari plugin for reading multiple microscopy and general image file formats directly into the viewer using pure Python.
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