Skip to content

pjl54/Util

Repository files navigation

Util

A set of tools that have helped me process whole-slide images, extract features from object segmentations, and build and evaluate machine learning models.

ROIextraction

Matlab code for extracting annotated regions of interest from whole-slide images. You need either BioFormats or Openslide for getROIfromTif to work at all and need both of them to get full functionality. Annotations can be read directly from .czi files or from .xml files in the Aperio ImageScope format for all other image types.

featureExtraction

Matlab code for extracting 216 morphology features from object segmentations and 26 Haralick texture features. CGT and sub-graph features are tuned for 1.25X (8MPP) segmentations.

lumenSegHelpers

Matlab functions for extracting regions of interest at a certain MPP and processing binary masks to get bounds structs which can be used in extract_all_features.m in featureExtraction.

bfmatlab

A fork of the bioformats matlab commands. Does not have the actual bioformats.jar. Included because I have modified bfopenSpecificLayer.m to work in getROIfromTif.

Visualization

Tools for visualizing segmentation results and model performance.

feature_stability

Code for calculating feature stability as described in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5076015/

About

No description, website, or topics provided.

Resources

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published