Segment Anything for Microscopy
segmentation cell-segmentation bioimage-analysis microscopy-images nuclei-segmentation napari segment-anything mitochondria-segmentation micro-sam
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Feb 27, 2026 - Jupyter Notebook
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microscopy-images
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Image segmentation - general superpixel segmentation & center detection & region growing
image-annotation image-processing medical-imaging ipynb region-growing graph-cut object-detection image-segmentation image-analysis superpixels shape-models microscopy-images superpixel-segmentation graph-cuts center-detection segmentation-pipeline biomedical-imaging ellipse-fitting
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Jan 4, 2022 - Python
nucleus/cell and histopathology image classification,detection,segmentation
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Dec 15, 2020
Our solution for ICIAR 2018 Grand Challenge
machine-learning computer-vision deep-learning healthcare microscopy-images iciar-challenge computer-aided-diagnosis
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Dec 16, 2020 - Python
Read and write Neuroglancer datasets programmatically.
python cloud big-data serverless numpy matrix s3 gcs mesh tensor electron-microscopy connectomics microscopy skeletons biomedical-image-processing volumetric-data microscopy-images neuroglancer large-image chunked-image
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Mar 6, 2026 - Python
Visualize, share and annotate your large 3D images online
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Mar 7, 2026 - TypeScript
A Python software library with a variety of functions for (optical) microscopy image restoration, reconstruction and analysis.
image-processing image-analysis fourier-analysis image-restoration microscopy-images image-resolution deconvolution-microscopy
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Aug 29, 2025 - Jupyter Notebook
Mastodon - a large-scale tracking and track-editing framework for large, multi-view images.
java imglib2 interactive-analysis interactive-visualizations tracking-algorithm bioimage-analysis microscopy-images large-images trackmate cell-lineage
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Feb 3, 2026 - Java
Creating figures and animations for multi-channel images with a focus on microscopy.
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Dec 16, 2024 - Jupyter Notebook
Particle tracking by solving linear assignment problem.
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Mar 6, 2026 - Python
Utils and convenience functions for large-scale bio-image analysis.
segmentation image-analysis affine-transformation bio-image-analysis multicut 3d-segmentation microscopy-images lifted-multicut mutex-watershed
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Mar 6, 2026 - Python
Generative Adversarial Network for single image super-resolution in high content screening microscopy images
computer-vision deep-learning image-reconstruction gan image-generation convolutional-neural-networks perceptual-losses super-resolution generative-adversarial-networks vgg19 srgan microscopy-images high-content-screening
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Jan 20, 2018 - Jupyter Notebook
Pure Python library for reading NIS Elements ND2 images and metadata
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Jan 15, 2025 - Python
ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.
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Nov 13, 2025 - Python
Distributed segmentation for bio-image-analysis
segmentation connectomics bio-image-analysis watershed cluster-computing multicut 3d-segmentation microscopy-images lifted-multicut mutex-watershed
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Jan 18, 2026 - Python
Label Free Prediction of Cell Painting from Brightfield Images
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Jul 7, 2022 - Python
A Python library for easily calculating image-quality related features from images
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Jul 6, 2023 - Python
Create web-based OME-Zarr galleries
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Nov 6, 2025 - Jupyter Notebook
img2vid
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Dec 14, 2022 - MATLAB
PiSCAT is a python-based package with a graphical user interface for performing high-performance analysis on a variety of iSCAT measurements.
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Aug 6, 2024 - Jupyter Notebook
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