Popular GitHub Repositories for Microscopy

Tools for computational pathology

cuCIM - RAPIDS GPU-accelerated image processing library

Image segmentation - general superpixel segmentation & center detection & region growing

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

Pipeline for particle picking in cryo-electron microscopy images using convolutional neural networks trained from positive and unlabeled examples. Also featuring micrograph and tomogram denoising with DNNs.

(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"

Encoder-Decoder Cell and Nuclei segmentation models

Official repo for Recursion's accepted spotlight paper at NeurIPS 2023 Generative AI & Biology workshop.

Generative Adversarial Network for single image super-resolution in high content screening microscopy images

Workflow for Simulation and Automatic Semantic Segmentation of Electron Microscopy Images

XLuminA, a highly-efficient, auto-differentiating discovery framework for super-resolution microscopy.

Multi-modal Image Registration And Connectivity anaLysis

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

Single-cell spatial proteomics analysis that makes you happy!

Label Free Prediction of Cell Painting from Brightfield Images

Utilities for building and using the CEM dataset for unsupervised pre-training and downstream tasks.

Easy Volumetric Segmentation with Deep Learning

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

Parameter Efficient Fine-Tuning of Segment Anything Model

[WACV 2024] AnyStar: Domain randomized universal star-convex 3D instance segmentation