mschumak Goto Github PK

01-shell_git_github

02-sql

03-python

04-r

alchemistpkg

Assignment 1 for the Building Research Software Course, January 2024

boxdrop

A facility to select a random region of interest with a predefined size

building_software

colormap

ColorMap Sedeen plugin, to overlay an intensity/probability map over a whole-slide image

createstainvectorprofile

Sedeen plugin to select stained regions using ROIs, and generate stain vector files from them

dsi-workshop-repo

exporttransformedroi

extensionsindex

Slicer extensions index

ink-wsi

Filters ink out of whole slide images. Potentially can also correct it

minimalplugin

Minimal code for a Sedeen plugin

opticaldensitythreshold

A Sedeen plugin that can apply thresholds based on optical density values

productionwork

A workspace for my work on the Production course with UofT DSI

projectweek2018

Shared work developed during Project Week at Western, 2018

qt-easy-build

Scripts allowing to easily build Qt with OpenSSL support on Linux, macOS or Windows

research-software-homework

Homework assignments for the UofT DSI Building Research Software course

rigidregistration

Rigid registration of the images

roicropper

This plugin extracts region of interest from pathology slides given their coordinates in an .xml file (by a pathologist) and save them in a separated image. It aslo creates corresponding mask based on annotations in the region of interest.

slicercustomapptemplate

Template to be used as a starting point for creating a custom 3D Slicer application

stainanalysis-plugin

This plugin calculates the percentage area of a region of interest which has been stained using an IHC biomarker.

tileextraction_plugin

Tile extraction plug-in is useful for sampling a large image for training, auto-encoders applications etc... It works based on principles of stereology.