smujiang

CalculateSUV

Matlab code for calculating SUV in PET images

CARN

Direct Automated Quantitative Measurement of Spine by Cascade Amplifier Regression Network with Manifold Regularization

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.

Cytomine_GetAnnotation

Pull annotations and the corrosponding image patches from a Cytomine server.

MxIF_DAPI_ref_QC

MxIF image quality checking

Re-stained_WSIs_Registration

Re-stained whole slide image alignment

TumorStromaReaction

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

WSI2DICOM

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

WSIPenMarkingRemoval

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

WSITools

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

smujiang/WSITools

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

smujiang/Re-stained_WSIs_Registration

Re-stained whole slide image alignment

smujiang/WSIPenMarkingRemoval

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

smujiang/WSI2DICOM

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

smujiang/CalculateSUV

Matlab code for calculating SUV in PET images

smujiang/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.

smujiang/TumorStromaReaction

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

smujiang/MxIF_DAPI_ref_QC

MxIF image quality checking

smujiang/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'

smujiang/cucim

smujiang/deep-graph-matching-consensus

Implementation of "Deep Graph Matching Consensus" in PyTorch

smujiang/DNABERT

DNABERT: Experimental Fork

smujiang/docs

IMPROVE

smujiang/DrugCell

A visible neural network model for drug response prediction

smujiang/gcp-for-bioinformatics

GCP for Bioinformatics Researchers

smujiang/HIPT

Hierarchical Image Pyramid Transformer - CVPR 2022 (Oral)

smujiang/HistoVAE

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

smujiang/invariant-haralick-features

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

smujiang/OpenGLInsightsCode

Source code for OpenGL Insights

smujiang/PianoSheets

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

smujiang/QuPath_Utility_Scripts

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

smujiang/research-method

论文写作与资料分享

smujiang/serving

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

smujiang/Singularity

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

smujiang/tcrp-reproduce

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

smujiang/TCRP_data

smujiang/TCRP_pipeline

smujiang/TGSA

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

smujiang/The_Handy_OMERO_Toolbox

An assortment of scripts used to interface with our internal instance of OMERO and accomplish custom tasks

smujiang/umap-explorer

An interactive UMAP visualization of the MNIST data set.