smujiang

WSITools

Tools for whole slide image (WSI) processing. Especially for (pairwise) patch extraction, annotation parsing and data preparation for deep learning purposes.

Re-stained_WSIs_Registration

Re-stained whole slide image alignment

WSIPenMarkingRemoval

Remove pen-marking annotations on whole slide images(WSIs) for data achiving.

WSI2DICOM

Simple prototype of converting whole slide image (WSI) to multiframe DICOM images

CalculateSUV

Matlab code for calculating SUV in PET images

CellularComposition

Interactive modules to digitally annotate H&E whole slide images, construct cell and tissue level features and classify cell types. Specifically for a case study of differentiating borderline and high-grade serous ovarian tumors.

TumorStromaReaction

Quantitatively evaluate tumor stroma reaction within ovarian cancers, and establish assocaitaions to prognosis, molecular signatures.

MxIF_DAPI_ref_QC

MxIF image quality checking

Adversarial-learning-of-cancer-tissue-representations

Corresponding code of 'Quiros, A. C., Coudray, N., Yeaton, A., Sunhem, W., Murray-Smith, R., Tsirigos, A., Yuan, K. Adversarial learning of cancer tissue representations. The 24th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2021'

cucim

deep-graph-matching-consensus

Implementation of "Deep Graph Matching Consensus" in PyTorch

DNABERT

DNABERT: Experimental Fork

docs

IMPROVE

DrugCell

A visible neural network model for drug response prediction

gcp-for-bioinformatics

GCP for Bioinformatics Researchers

HIPT

Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)

HistoVAE

This repository contains work towards HistoVAE: creating meaningful representations of Histopathology images using Variational Autoencoders.

invariant-haralick-features

Matlab and python code (coming soon) for calculating the invariant Haralick features.

OpenGLInsightsCode

Source code for OpenGL Insights

PianoSheets

Piano sheets from Kyle Landry, vkgoeswild, Beethoven, Yiruma, Zohar002, etc.

Pytorch-UNet

PyTorch implementation of the U-Net for image semantic segmentation with high quality images

QuPath_Utility_Scripts

a bunch of independent scripts to perform tasks within QuPath to aid in cell classification & other utility

research-method

论文写作与资料分享

serving

A flexible, high-performance serving system for machine learning models

Singularity

Singularity definitions that can be extended to support execution of community models.

tcrp-reproduce

Attempting to reproduce TCRP by adhering as close as positive to the original code

TCRP_data

TCRP_pipeline

TGSA

PyTorch implementation of <<TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation>>

Thread-Portrait

Here is the code I used to make my Thread Portrait.