Biological Image Analysis
144 items from hallvaaw/awesome-biological-image-analysis ★198
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LeafByte zoegp.science
Free and open source mobile app for measuring herbivory quickly and accurately.
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YeastMate yeastmate.readthedocs.io
Neural network-assisted segmentation of mating and budding events in S. cerevisiae.
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VisionSetil visionsetil.com
Multi-view image classification of Iberian mushrooms for education (open encyclopedia of 523 taxa, deadly lookalikes). Orientation only — never consumption permission.
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TissUUmaps tissuumaps.github.io
Visualizer of NGS data, plot millions of points and interact, gate, export. ISS rounds and base visualization.
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Trackpy soft-matter.github.io
Fast and Flexible Particle-Tracking Toolkit.
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QuPath qupath.github.io
Open source software for digital pathology image analysis.
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RhizoTrak prbio-hub.github.io
Open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images.
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Orbit orbit.bio
A versatile image analysis software for biological image-based quantification using machine learning, especially for whole slide imaging.
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Large-scale image-based screening and profiling of cellular phenotypes onlinelibrary.wiley.com
A workflow for phenotype extraction from high throughput imaging experiments.
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Panda nitrc.org
Pipeline for Analyzing braiN Diffusion imAges: A MATLAB toolbox for pipeline processing of diffusion MRI images.
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MorphoGraphX morphographx.org
Open source application for the visualization and analysis of 4D biological datasets.
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PaCeQuant mitobo.informatik.uni-halle.de
An ImageJ-based tool which provides a fully automatic image analysis workflow for PC shape quantification.
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Biobeam maweigert.github.io
Open source software package that is designed to provide fast methods for in-silico optical experiments with an emphasize on image formation in biological tissues.
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Workflow and metrics for image quality control in large-scale high-content screens linkinghub.elsevier.com
Approaches for quality control in high-content imaging screens.
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NeuronJ imagescience.org
An ImageJ plugin for neurite tracing and analysis.
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TraJClassifier imagej.net
Fiji plugin that loads trajectories from TrackMate, characterizes them using TraJ and classifiies them into normal diffusion, subdiffusion, confined diffusion and directed/active motion by a random forest approach (through Renjin).
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PAT-GEOM ianzwchan.com
A software package for the analysis of animal colour pattern.
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HistoPLUS huggingface.co
Pre-trained model for cell nuclei segmentation and classification in histology images.
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TracX gitlab.com
MATLAB generic toolbox for cell tracking from various microscopy image modalities such as Bright-field (BF), phase contrast (PhC) or fluorescence (FL) with an automated track quality assessment in absence of a ground truth.
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Icy github.com
Open community platform for bioimage informatics, providing software resources to visualize, annotate and quantify bioimaging data.
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BABY git.ecdf.ed.ac.uk
An image processing pipeline for accurate single-cell growth estimation of budding cells from bright-field stacks.
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A Hitchhiker's guide through the bio-image analysis software universe febs.onlinelibrary.wiley.com
An article presenting a curated guide and glossary of bio-image analysis terms and tools.
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Biological imaging software tools dx.doi.org
The steps of biological image analysis and the appropriate tools for each step.
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BiofilmQ drescherlab.org
Advanced biofilm analysis tool for quantifying the properties of cells inside large 3-dimensional biofilm communities in space and time.
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BacStalk drescherlab.org
Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species.
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Data-analysis strategies for image-based cell profiling doi.org
In-detail explanations of image analysis pipelines.
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CLIJ2 clij.github.io
GPU-accelerated image processing library for ImageJ/Fiji, Icy, MATLAB and Java.
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PyScratch bitbucket.org
Open source tool that autonomously performs quantitative analysis of in vitro scratch assays.
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BiaPy biapyx.github.io
Open source ready-to-use all-in-one library that provides deep-learning workflows for a large variety of bioimage analysis tasks.
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Vaa3D alleninstitute.org
Open-source software for 3D/4D/5D image visualization and analysis.
