Biological Image Analysis
144 items from hallvaaw/awesome-biological-image-analysis ★198
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TrackMate github.com
User-friendly interface that allows for performing tracking, data visualization, editing results and track analysis in a convenient way.
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Cellfinder github.com
Automated 3D cell detection and registration of whole-brain images.
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AtomAI github.com
PyTorch-based package for deep/machine learning analysis of microscopy data.
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AICSImageIO github.com
Image reading, metadata conversion, and image writing for nicroscopy images in Python.
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CellSAM github.com
A foundation model for cell segmentation trained on a diverse range of cells and data types.
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Ultrack github.com
Versatile cell tracking method for 2D, 3D, and multichannel timelapses, overcoming segmentation challenges in complex tissues.
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Usiigaci github.com
Stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning.
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PyTorch Connectomics github.com
Deep learning framework for automatic and semi-automatic annotation of connectomics datasets, powered by PyTorch.
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Cell-ACDC github.com
A GUI-based Python framework for segmentation, tracking, cell cycle annotations and quantification of microscopy data.
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CaPTk github.com
Cancer Imaging Phenomics Toolkit: A software platform to perform image analysis and predictive modeling tasks.
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Proseg github.com
A cell segmentation method for in situ spatial transcriptomics.
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BG-atlasAPI github.com
A lightweight Python module to interact with atlases for systems neuroscience.
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CloudVolume github.com
Read and write Neuroglancer datasets programmatically.
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OAD github.com
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools.
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CellProfiler Analyst github.com
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
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Brainreg github.com
Automated 3D brain registration with support for multiple species and atlases.
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Picasso github.com
A collection of tools for painting super-resolution images.
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FastPathology github.com
Open-source software for deep learning-based digital pathology.
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Spotiflow github.com
A deep learning-based, threshold-agnostic, and subpixel-accurate spot detection method developed for spatial transcriptomics workflows.
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Pycytominer github.com
Data processing functions for profiling perturbations.
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PAQUO github.com
A library for interacting with QuPath from Python.
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PlantSeg github.com
Tool for cell instance aware segmentation in densely packed 3D volumetric images.
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AxonDeepSeg github.com
Segment axon and myelin from microscopy data using deep learning.
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MorpholibJ github.com
Collection of mathematical morphology methods and plugins for ImageJ.
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Trainable Weka Segmentation github.com
Fiji plugin and library that combines a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations.
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FlashDeconv github.com
High-performance spatial transcriptomics deconvolution (~1M spots in ~3 min).
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ThunderSTORM github.com
A comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging.
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Ark-Analysis github.com
A pipeline toolbox for analyzing multiplexed imaging data.
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PYME github.com
Open-source application suite for light microscopy acquisition, data storage, visualization, and analysis.
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Nellie github.com
Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy.
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Wholebrain github.com
Automated cell detection and registration of whole-brain images with plot of cell counts per region and Hemishpere.
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Pyotf github.com
A simulation software package for modelling optical transfer functions (OTF)/point spread functions (PSF) of optical microscopes written in Python.
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RootPainter github.com
Deep learning segmentation of biological images with corrective annotation.
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SMAP github.com
A modular super-resolution microscopy analysis platform for SMLM data.
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NeuroAnatomy Toolbox github.com
R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
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Big-fish github.com
Python package for the analysis of smFISH images.
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EBImage github.com
Image processing toolbox for R.
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SplineDist github.com
Object detection with spline curves.
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DeepMushroom github.com
Image classification of fungus using ResNet.
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MAPS github.com
MAPS (Machine learning for Analysis of Proteomics in Spatial biology) is a machine learning approach facilitating rapid and precise cell type identification with human-level accuracy from spatial proteomics data.
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SNT github.com
ImageJ framework for semi-automated tracing and analysis of neurons.
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Minerva github.com
Image viewer designed specifically to make it easy for non-expert users to interact with complex tissue images.
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GPim github.com
Gaussian processes and Bayesian optimization for images and hyperspectral data.
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RS-FISH github.com
Fiji plugin to detect FISH spots in 2D/3D images which scales to very large images.
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ThermImageJ github.com
ImageJ functions and macros for working with thermal image files.
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Aradeepopsis github.com
A versatile, fully open-source pipeline to extract phenotypic measurements from plant images.
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Nd2reader github.com
A pure-Python package that reads images produced by NIS Elements 4.0+.
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TrailMap github.com
Software package to extract axonal data from cleared brains.
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ZetaStitcher github.com
Tool designed to stitch large volumetric images such as those produced by light-sheet fluorescence microscopes.
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NEFI2 github.com
Python tool created to extract networks from images.
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