ImageProcessing

Code for analyzing microscopy images. Developed by the Warmflash lab at Rice University

Overview

Useful Routines

High level scripts

analyseOneColonyOneImageLSM

Data classes

Metadata - useful for storing information about image
MetadataMicropattern - metadata subclass for micropatterned experiment

Utilities

Max Intensity
bfMaxIntensity - make max intensity from bioformats reader mkMaxIntensity - run on file to output max intensity file to disk
mkMaxIntensities - run on whole directory to make max intensity images
splitLargeImageFile - split big tiled image to smaller ones for analysis

Image Correction
smoothAndBackgroundSubtractOneImage - apply gaussian filter and subtract background

Input output
readIlastikFile - reads output binary masks (h5 format) from Ilastik readImageDir - read a directory of images into cell array. options for selection by string

Visualization
compareMultiChannelImages - show composite image. multiple channels, multiple conditions. consistent lookup table