Pinned Repositories
Phindr3D
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
CreateStainVectorProfile
Sedeen plugin to select stained regions using ROIs, and generate stain vector files from them
StainAnalysis-plugin
This plugin calculates the percentage area of a region of interest which has been stained using an IHC biomarker.
mschumak's Repositories
mschumak/CreateStainVectorProfile
Sedeen plugin to select stained regions using ROIs, and generate stain vector files from them
mschumak/StainAnalysis-plugin
This plugin calculates the percentage area of a region of interest which has been stained using an IHC biomarker.
mschumak/01-shell_git_github
mschumak/02-sql
mschumak/03-python
mschumak/04-r
mschumak/alchemistpkg
Assignment 1 for the Building Research Software Course, January 2024
mschumak/BoxDrop
A facility to select a random region of interest with a predefined size
mschumak/building_software
mschumak/ColorMap
ColorMap Sedeen plugin, to overlay an intensity/probability map over a whole-slide image
mschumak/ExportTransformedROI
mschumak/ExtensionsIndex
Slicer extensions index
mschumak/Ink-WSI
Filters ink out of whole slide images. Potentially can also correct it
mschumak/OpticalDensityThreshold
A Sedeen plugin that can apply thresholds based on optical density values
mschumak/DSI-workshop-repo
mschumak/MinimalPlugin
Minimal code for a Sedeen plugin
mschumak/productionwork
A workspace for my work on the Production course with UofT DSI
mschumak/ProjectWeek2018
Shared work developed during Project Week at Western, 2018
mschumak/qt-easy-build
Scripts allowing to easily build Qt with OpenSSL support on Linux, macOS or Windows
mschumak/research-software-homework
Homework assignments for the UofT DSI Building Research Software course
mschumak/RigidRegistration
Rigid registration of the images
mschumak/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.
mschumak/SlicerCustomAppTemplate
Template to be used as a starting point for creating a custom 3D Slicer application
mschumak/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.