microscopy
There are 521 repositories under microscopy topic.
BMIRDS/deepslide
Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.
3dem/relion
Image-processing software for cryo-electron microscopy
Dana-Farber-AIOS/pathml
Tools for computational pathology
rapidsai/cucim
cuCIM - RAPIDS GPU-accelerated image processing library
pycroscopy/pycroscopy
Scientific analysis of nanoscale materials imaging data
clEsperanto/pyclesperanto_prototype
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
AllenCellModeling/aicsimageio
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
pycroscopy/atomai
Deep and Machine Learning for Microscopy
brainglobe/cellfinder
Automated 3D cell detection in very large images
zudi-lin/pytorch_connectomics
PyTorch Connectomics: segmentation toolbox for EM connectomics
TIO-IKIM/CellViT
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
seung-lab/cloud-volume
Read and write Neuroglancer datasets programmatically.
scalableminds/webknossos
Visualize, share and annotate your large 3D images online
zeiss-microscopy/OAD
Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.
brainglobe/brainglobe-atlasapi
A lightweight python module to interact with atlases for systems neuroscience
axondeepseg/axondeepseg
Axon/Myelin segmentation using Deep Learning
brainglobe/brainreg
Automated 3D brain registration with support for multiple species and atlases.
jungmannlab/picasso
A collection of tools for painting super-resolution images
hallvaaw/awesome-biological-image-analysis
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
dancsalo/TensorFlow-MIL
TF Implementation of Multiple Instance Learning FCN.
TuragaLab/DECODE
This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
oanegros/tif2blender
Loading and handling microscopy data in blender
WeisongZhao/Sparse-SIM
Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3
zeiss-microscopy/libCZI
Open Source Cross-Platform C++ library to read CZI image files
royerlab/cytoself
Self-supervised models for encoding protein localization patterns from microscopy images
cytomining/pycytominer
Python package for processing image-based profiling data
david-hoffman/pyotf
python functions for simulating optical transfer functions
okunator/cellseg_models.pytorch
Encoder-Decoder Cell and Nuclei segmentation models
yijiang1/fold_slice
Electron/X-ray ptychography and tomography/laminography
ImSwitch/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.
NICALab/SUPPORT
Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.
tlambert03/FPbase
The Fluorescent Protein Database
pymmcore-plus/napari-micromanager
GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets
ziatdinovmax/GPim
Gaussian processes and Bayesian optimization for images and hyperspectral data
PlanktoScope/PlanktoScope
Open and Affordable Quantitative Imaging Platform
roflmaostc/DeconvOptim.jl
A multi-dimensional, high performance deconvolution framework written in Julia Lang for CPUs and GPUs.