cellfinderAutomated 3D cell detection and registration of whole-brain images
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ome-typesnative Python dataclasses for the OME data model
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impySpeed up coding/extending image analysis in Python.
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axondeepsegAxon/Myelin segmentation using Deep Learning
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cellpose-naparinapari plugin for cellpose (see www.cellpose.org) - an anatomical segmentation tool
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odemisOpen Delmic Microscope Software
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MiM NikonTiConfig and scripts used to run a Nikon Eclipse Ti in the vanNimwegen lab.
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sparse-deconv-pyOfficial Python implementation of the 'Sparse deconvolution'-v0.3.0
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segmentationCode for my master's thesis. Instance segmentation of fluorescence microscopy images with deep learning.
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picassoA collection of tools for painting super-resolution images
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ImSwitchImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.
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brainregAutomated 3D brain registration with support for multiple species and atlases.
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cucimNo description or website provided.
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arboretumTrack and lineage visualization with btrack and Napari
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MicroscPSF-PyFast and Accurate 3D PSF Computation for Fluorescence Microscopy
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ColiCoordsSingle-cell fluorescence microscopy data analysis
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SwiftyImageIOA swift wrapper around ImageIO framework
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quadartPython module for producing quad-tree art
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DeconvolutionLab2Java (ImageJ/Fiji) software package for 3D deconvolution microscopy
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simple sim fusion demoSimple demo of structured illumination microscopy image fusion via Richardson-Lucy deconvolution
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flikaAn interactive image processing program for biologists written in Python.
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atomaiDeep and Machine Learning for Microscopy
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LLSpyLattice light-sheet post-processing utility.
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brainreg-segmentSegmentation of 3D shapes in a common anatomical space
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