Discover @smujiang Open Source projects

Jun Jiang (@smujiang)

smujiang

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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

ObjectDetectionAPIGuide

A self summarized tutorial for Object detection API. https://github.com/tensorflow/models/tree/master/research/object_detection

Cytomine_Python_Client-0.1.4_for_python_3.6

This is a installation package of Cytomine_Python_Client-0.1.4 for python 3.6. The original one is just compatible with python 2.7, which can be cloned from https://github.com/cytomine/Cytomine-python-client

Cytomine_GetAnnotation

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