Code for analyzing microscopy images. Developed by the Warmflash lab at Rice University
analyseOneColonyOneImageLSM
Metadata - useful for storing information about image
MetadataMicropattern - metadata subclass for micropatterned experiment
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