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BMIRDS /deepslide

Star503

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.

cancer resnet microscopy sliding-windows lung wsi medical-image-analysis pathology-image histopathology-images

UpdatedJun 7, 2024
Python

3dem /relion

Star467

Image-processing software for cryo-electron microscopy

gui hpc molecular-structures cuda image-processing nvidia high-performance-computing graphics-programming ctf regularization cryo-em microscopy likelihood maximum-likelihood optimization-algorithms relion molecular-biology atomistic-models biomolecular-dynamics microscope

UpdatedMar 22, 2025
C++

Dana-Farber-AIOS /pathml

Star417

Tools for computational pathology

python machine-learning research deep-learning pytorch image-analysis microscopy biomedical-image-processing fluorescence-microscopy-imaging digital-pathology pathology computational-pathology spatial-transcriptomics histopathology pathml

UpdatedFeb 11, 2025
Python

rapidsai /cucim

Star387

cuCIM - RAPIDS GPU-accelerated image processing library

computer-vision gpu cuda image-processing nvidia medical-imaging segmentation image-analysis microscopy digital-pathology image-data multidimensional-image-processing

UpdatedMar 21, 2025
Jupyter Notebook

TIO-IKIM /CellViT

Star280

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

python ai ml pytorch cell microscopy digitalpathology

UpdatedJan 10, 2025
Python

pycroscopy /pycroscopy

Star263

Scientific analysis of nanoscale materials imaging data

visualization atom machine-learning statistics afm signal-processing stm fft electron-microscopy stem materials-science scanning microscopy imaging spectroscopy infrared raman atomic-force-microscopy scanning-probe-microscopy scanning-tunnelling-microscopy

UpdatedMar 7, 2025
Jupyter Notebook

clEsperanto /pyclesperanto_prototype

Star219

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

gpu-acceleration microscopy bioimage-analysis

UpdatedFeb 21, 2025
Jupyter Notebook

AllenCellModeling /aicsimageio

Star211

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

python xarray scientific-computing imageio bio-formats dask image-metadata microscopy scientific-formats

UpdatedJan 15, 2025
Python

pycroscopy /atomai

Star208

Deep and Machine Learning for Microscopy

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

UpdatedJun 26, 2024
Python

DeepTrackAI /DeepTrack2

Star194

DeepTrack2 is a modular Python library for generating, manipulating, and analyzing image data pipelines for machine learning and experimental imaging.

machine-learning deep-learning image-processing optics microscopy data-augmentation biophysics soft-matter computational-pipelines photonics superresolution