Biological Image Analysis
144 items from hallvaaw/awesome-biological-image-analysis ★198
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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.
