Microscope image processing deals with the acquisition, enhancement, visualization and analysis of images generated by a wide variety of microscope technologies. Microscopy is used in manufacturing, life sciences, geosciences, materials sciences and more. Automated and interactive processing of microscope data can lead to more vivid and informative images and yields quantitative measurements. The Wolfram Language provides extensive support for acquiring and accessing microscope data and metadata, as well as a comprehensive suite of functionality to enhance images, reconstruct 3D objects and analyze microscopy images via segmentation, measurements, statistical models and neural networks for recognition.

Image Acquisition »

Import — import data and metadata from standard formats (TIFF, OME-TIFF, DICOM, ...) and proprietary formats (Leica, Zeiss, Olympus, ...) through BioFormatsLink

CurrentImage — capture an image or video in real time from a microscope camera

Combining Images

ImageAlign — align images from a stack or grid of images

Image3D  ▪  ImageFocusCombine  ▪  FindGeometricTransform

Brightness & Color Enhancement »

BrightnessEqualize — correct uneven brightness

ImageAdjust  ▪  HistogramTransform  ▪  ...

Denoising and Image Restoration »

ImageDeconvolve — remove blur induced by a point spread function (PSF)

MeanFilter  ▪  TotalVariationFilter  ▪  CurvatureFlowFilter  ▪  Inpaint  ▪  ...

Image Properties »

ImageMeasurements — measure shape and color properties of an image

ImageHistogram  ▪  Image3DProjection  ▪  Image3DSlices  ▪  ...

Segmentation Analysis »

Binarize — segmentation by thresholding pixel intensities

ClusteringComponents — segmentation based on cluster analysis (-means, etc.)

ComponentMeasurements  ▪  SelectComponents  ▪  DeleteSmallComponents  ▪  ...

Feature Extraction & Tracking »

ImageDisplacements — dense tracking of pixels across a sequence of images

ImageFeatureTrack  ▪  ImageKeypoints  ▪  ImageCorrespondingPoints  ▪  ...

Classification & Feature Detection »

Classify — categorize images or components

FeatureExtract  ▪  FeatureSpacePlot  ▪  FindClusters  ▪  ...

NetGraph  ▪  NetChain  ▪  NetTrain  ▪  NetModel  ▪  NetEncoder  ▪  ...

Visualization »

DynamicImage — explore an image by zooming and panning

HighlightImage  ▪  Colorize  ▪  ListAnimate  ▪  ListContourPlot3D  ▪  ...