kheffah
Pathology resident physician at Northwestern University, with an MD from Cairo University and PhD from Emory University. I work in Computational Pathology.
Northwestern UniversityChicago, IL, USA
Pinned Repositories
HistomicsTK
A Python toolkit for pathology image analysis algorithms.
histolab
Library for Digital Pathology Image Processing
ExtendingRipleysK
Extending Ripley’s K-Function to Quantify Aggregation in 2-D Grayscale Images
Healthcare-Database-APIs
Tools for interaction with various healthcare databases, including CDC, chicagohealthatlas etc
StainTools
Tools for tissue image stain normalization and augmentation in Python 3. [python, scientific]
tensorflow_FCN8Workflow
BCSS
Use this to download all elements of the BCSS dataset described in: Amgad M, Elfandy H, ..., Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz083
kheffah's Repositories
kheffah/tensorflow_FCN8Workflow
kheffah/Healthcare-Database-APIs
Tools for interaction with various healthcare databases, including CDC, chicagohealthatlas etc
kheffah/StainTools
Tools for tissue image stain normalization and augmentation in Python 3. [python, scientific]
kheffah/ActiveLearning
Software and documentation from the active learning project on interactive classification.
kheffah/BayesianOptimization
A Python implementation of global optimization with gaussian processes.
kheffah/code_snippets
kheffah/crowd_truth_infer
This is the framework with 17 existing crowdsourced truth inference algorithms.
kheffah/Detectron
FAIR's research platform for object detection research, implementing popular algorithms like Mask R-CNN and RetinaNet.
kheffah/digital_slide_archive
The official deployment of the Digital Slide Archive and HistomicsTK.
kheffah/FastMaskRCNN
Mask RCNN in TensorFlow
kheffah/Fully-Connected-DenseNets-Semantic-Segmentation
Fully Connected DenseNet for Image Segmentation (https://arxiv.org/pdf/1611.09326v1.pdf)
kheffah/hickle
a HDF5-based python pickle replacement
kheffah/HistoQC
HistoQC is an open-source quality control tool for digital pathology slides
kheffah/imagecluster
Cluster images based on image content using a pre-trained deep neural network and hierarchical clustering
kheffah/intro-git-demo
This code is for an introduction to Git at Emory University.
kheffah/Mask_RCNN
Mask R-CNN for object detection and instance segmentation on Keras and TensorFlow
kheffah/metagenome_assignment
kheffah/MINNs
Codes for our paper "Revisiting Multiple Instance Neural Networks".
kheffah/misvm
Multiple-Instance Support Vector Machines
kheffah/neuralnets
Deep Learning libraries tested on images and time series
kheffah/nvidia-docker
Build and run Docker containers leveraging NVIDIA GPUs
kheffah/pydensecrf
Python wrapper to Philipp Krähenbühl's dense (fully connected) CRFs with gaussian edge potentials.
kheffah/pytorch_tutorial
PyTorch tutorial for PyData Berlin
kheffah/stanford-cs-230-deep-learning
VIP cheatsheets for Stanford's CS 230 Deep Learning
kheffah/tensorflow-fcn
An Implementation of Fully Convolutional Networks in Tensorflow.
kheffah/TensorFlow-MIL
TF Implementation of Multiple Instance Learning FCN.
kheffah/tfwss
Weakly Supervised Segmentation with Tensorflow. Implements instance segmentation as described in Simple Does It: Weakly Supervised Instance and Semantic Segmentation, by Khoreva et al. (CVPR 2017).
kheffah/TILsAuthors
kheffah/ultrasound-nerve-segmentation
Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras
kheffah/unet
unet for image segmentation