dgutman Goto Github PK

adrc-clustering

adrc_analytics

Scripts to pull data from PUBMED and generate statistics for the Emory ADRC

adrcpathviewer

This is a development workspace for a pathology viewer for the ADRC @ Emory using the DSA CodeBase

computablebrain-dhtml

This is the computable brain DHTML version

covalic

Application for hosting challenges

d3-force-directed-graph

Contains all examples of our "Interactive & Dynamic Force-Directed Graphs with D3" blog post

dg-ndpitools

A collection of utilitites to tile and thumb NDPI files, a proprietary file format from Hamamatsu

dg-openslide-svstools

This is a set of tools I am using in openslide to tile images into squares at a given magnification, original C implementation also included

dg-xnat-tools

Various XNAT perl/bash scripts I have written to interact with XNAT client

digitalslidearchive

This is an open source version of the Cancer Digital Slide Archive (CDSA); a whole slide viewing application

docker-flask-mongodb-example

Uses docker compose with a python flask microservice and MongoDB instance to make a sample application

dsa-annotation-reviewer

These are lightweight Jupyter notebook and/or dash examples pulling and generating annotations in a DSA friendly format

dsa_cbir_prototypes

Prototypes for Content Based Image Retrieval using Deep Learning and Girder as the data store

dsa_faceted_search

Faceted Search using Webix, MongoDB to provide simple search UI

dsa_reg

dsa_slidelabeler

This app will scan an image from a digital slide, upload the slide to a REDCap instance, and then try and do OCR

dsa_tcga_webix_app

Digital Slide Archive App for TCGA data using the WEBIX UI

dsa_utils

Scripts and small apps developed to interact with the Digital Slide Archive

dsademonotebooks

Creating place for simple DSA helper functions and notebooks

dsalargeimageserver

Serves large image files as DZI files, with some other functionality for image QC

dsapostgisdev

Working on a prototype where I use PostGIS as the backend to storage annotation data for images in the Digital Slide Archive

dsasuperpixelannotator

This is a front end and back end system to generate superpixels for large image data and then build a tool to use superpixel based annotation

easymultirater_webixjet

fibrosis_code

Cleaned up codeset used in Fibrosis Quantification project.

flaskocrservice

Containerized service that should run OCR on an image so I can integrate with the DSA

gbm_deeplearning

gutmanlab-tools

These are various scripts generated by me and colleagues for managing XNAT, cleaning up data, brain tumor segmentatino ,etc

gutmanlabdockers

Creating Docker build scripts for various projects in my lab

gutmanlabdocumentation

Consolidating all the various documentation I have (badly) generated into a single repository

gutmanlabnipypeworkflows

Generating a repo for various workflows used in my lab that leverage NiPype