microscopy
There are 574 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
TIO-IKIM/CellViT
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
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
brainglobe/cellfinder
Automated 3D cell detection in very large images
pycroscopy/atomai
Deep and Machine Learning for Microscopy
DeepTrackAI/DeepTrack2
DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.
zudi-lin/pytorch_connectomics
PyTorch Connectomics: segmentation toolbox for EM connectomics
brainglobe/brainglobe-atlasapi
A Python interface to access neuroanatomical atlases
scalableminds/webknossos
Visualize, share and annotate your large 3D images online
seung-lab/cloud-volume
Read and write Neuroglancer datasets programmatically.
hallvaaw/awesome-biological-image-analysis
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
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/brainreg
Automated 3D brain registration with support for multiple species and atlases.
axondeepseg/axondeepseg
Axon/Myelin segmentation using Deep Learning
jungmannlab/picasso
A collection of tools for painting super-resolution images
oanegros/MicroscopyNodes
Loading and handling microscopy data in blender
cytomining/pycytominer
Python package for processing image-based profiling data
TuragaLab/DECODE
This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)
bioio-devs/bioio
Image reading, metadata management, and image writing for Microscopy images in Python
WeisongZhao/Sparse-SIM
Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3
okunator/cellseg_models.pytorch
Encoder-Decoder Cell and Nuclei segmentation models
dancsalo/TensorFlow-MIL
TF Implementation of Multiple Instance Learning FCN.
yijiang1/fold_slice
Electron/X-ray ptychography and tomography/laminography
NICALab/SUPPORT
Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.
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.
royerlab/cytoself
Self-supervised models for encoding protein localization patterns from microscopy images
PlanktoScope/PlanktoScope
Open and Affordable Quantitative Imaging Platform
david-hoffman/pyotf
python functions for simulating optical transfer functions
zeiss-microscopy/libCZI
Open Source Cross-Platform C++ library to read CZI image files
google-research/sofima
Scalable Optical Flow-based Image Montaging and Alignment
tlambert03/FPbase
The Fluorescent Protein Database