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Top 27 microscopy open source projects

DeconvolutionLab2

Java (ImageJ/Fiji) software package for 3D deconvolution microscopy

✭ 29

java algorithms microscopy 3d deconvolution images-plugins

simple sim fusion demo

Simple demo of structured illumination microscopy image fusion via Richardson-Lucy deconvolution

✭ 13

python demo microscopy simulated-data image-fusion richardson-lucy-deconvolution

remote refocus

A scientific publication, describing a way to improve microscopy. This repository hosts everything you need to reproduce our results. Read the publication here: https://andrewgyork.github.io/remote_refocus/

✭ 13

python HTML CSS javascript hardware hardware-designs scientific-publications microscopy

NanoJ-Fluidics

Manual, source-code and binaries for the NanoJ-Fluidics project

✭ 47

java C++automation storm electronics lego pump microscopy super-resolution fluidics live-cell high-content dna-paint

flika

An interactive image processing program for biologists written in Python.

✭ 20

python imagej image-processing neurons fluorescence microscopy calcium biologists astrocytes

Scripts

🔬🍸 Home of the ImageJ BAR: A collection of Broadly Applicable Routines for ImageJ

✭ 18

java ImageJ Macro python groovy javascript ruby imagej imagej2 scripts-collection scientific-workflows image-analysis microscopy jython beanshell ijm

bg-atlasapi

A lightweight python module to interact with atlases for systems neuroscience

✭ 54

Jupyter Notebook python visualisation neuroscience registration microscopy brain atlases

GPim

Gaussian processes and Bayesian optimization for images and hyperspectral data

✭ 29

python Dockerfile image-processing microscopy gaussian-processes bayesian-optimization colab-notebook hyperspectral-images lattice-models

atomai

Deep and Machine Learning for Microscopy

✭ 77

python machine-learning deep-learning materials jupyter-notebook pytorch ensemble-learning electron-microscopy materials-science microscopy semantic-segmentation fully-convolutional-networks multivariate-analysis variational-autoencoders deep-kernel-learning scanning-probe-microscopy google-colaboratory

LLSpy

Lattice light-sheet post-processing utility.

✭ 19

python image-processing image-analysis microscopy light-sheet

napari-aicsimageio

Multiple file format reading directly into napari using pure Python

✭ 18

python Makefile imageio microscopy napari

cellfinder

Automated 3D cell detection and registration of whole-brain images

✭ 122

python Dockerfile deep-learning neuroscience registration image-analysis microscopy imaging neuroanatomy cell-detection

OAD

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

✭ 90

Jupyter Notebook python matlab Batchfile Dockerfile ImageJ Macro open-source workflow machine-learning automation python-script image-processing zen acquisition image-analysis microscopy imaging zen-blue oad

ome-types

native Python dataclasses for the OME data model

✭ 28

python metadata microscopy ome

micromanager-samples

Python samples for Micro-Manager: image acquisition and microscope control system

✭ 19

python microscopy image-acquisition

axondeepseg

Axon/Myelin segmentation using Deep Learning

✭ 102

python Jupyter Notebook Dockerfile machine-learning deep-learning segmentation convolutional-neural-networks electron-microscopy axon microscopy myelin spinalcord histology neuropoly

odemis

Open Delmic Microscope Software

✭ 32

python shell HTML NSIS cython javascript microscopy

MiM NikonTi

Config and scripts used to run a Nikon Eclipse Ti in the vanNimwegen lab.

✭ 16

C++microscopy micro-manager nikon-eclipse-ti

sparse-deconv-py

Official Python implementation of the 'Sparse deconvolution'-v0.3.0

✭ 18

python image-processing microscopy super-resolution image-restoration fluorescence-microscopy-imaging

segmentation

Code for my master's thesis. Instance segmentation of fluorescence microscopy images with deep learning.

✭ 38

Jupyter Notebook tensorflow keras image-segmentation microscopy

picasso

A collection of tools for painting super-resolution images

✭ 77

python microscopy super-resolution dna-paint smlm

ImSwitch

ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.

✭ 43

python TeX fluorescence microscopy super-resolution

brainreg

Automated 3D brain registration with support for multiple species and atlases.

✭ 73

python neuroscience registration microscopy brain neuroanatomy atlases

cucim

No description or website provided.

✭ 218