---
title: "Image Computation for Microscopy"
language: "en"
type: "Guide"
summary: "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."
sections: 
  - 
    title: "Image Acquisition"
    link: "paclet:guide/CreatingAndImportingImages"
  - 
    title: "Combining Images"
    link: "null"
  - 
    title: "Brightness & Color Enhancement"
    link: "paclet:guide/ColorProcessing"
  - 
    title: "Denoising and Image Restoration"
    link: "paclet:guide/ImageRestoration"
  - 
    title: "Image Properties"
    link: "paclet:guide/ImageRepresentation"
  - 
    title: "Segmentation Analysis"
    link: "paclet:guide/SegmentationAnalysis"
  - 
    title: "Feature Extraction & Tracking"
    link: "paclet:guide/FeatureDetection"
  - 
    title: "Classification & Feature Detection"
    link: "paclet:guide/ComputerVision"
  - 
    title: "Visualization"
    link: "paclet:guide/DataVisualization"
keywords: 
- microscopy
- microscope
- microanalysis
- micro analysis
- microscope image processing
- micro analysis
- micro scale analysis
- computational microscopy
- image computation for microscopy
- brightness equalization
- image enhancement
- image filtering
- image segmentation
- interactive image analysis
- focus stacking
- 3D reconstruction
- image tracking
- image deconvolution
- color deconvolution
- biological science
- material science
- life science
canonical_url: "https://reference.wolfram.com/language/guide/ImageComputationForMicroscopy.html"
source: "Wolfram Language Documentation"
related_guides: 
  - 
    title: "Image Processing & Analysis"
    link: "https://reference.wolfram.com/language/guide/ImageProcessing.en.md"
  - 
    title: "Computer Vision"
    link: "https://reference.wolfram.com/language/guide/ComputerVision.en.md"
  - 
    title: "Machine Learning"
    link: "https://reference.wolfram.com/language/guide/MachineLearning.en.md"
  - 
    title: "Computational Photography"
    link: "https://reference.wolfram.com/language/guide/ComputationalPhotography.en.md"
related_workflow_guides: 
  - 
    title: "Specific Application Areas"
    link: "https://reference.wolfram.com/language/workflowguide/SpecificApplicationAreas.en.md"
related_functions: 
  - 
    title: "Binarize"
    link: "https://reference.wolfram.com/language/ref/Binarize.en.md"
  - 
    title: "BrightnessEqualize"
    link: "https://reference.wolfram.com/language/ref/BrightnessEqualize.en.md"
  - 
    title: "Classify"
    link: "https://reference.wolfram.com/language/ref/Classify.en.md"
  - 
    title: "ClusteringComponents"
    link: "https://reference.wolfram.com/language/ref/ClusteringComponents.en.md"
  - 
    title: "Colorize"
    link: "https://reference.wolfram.com/language/ref/Colorize.en.md"
  - 
    title: "ComponentMeasurements"
    link: "https://reference.wolfram.com/language/ref/ComponentMeasurements.en.md"
  - 
    title: "CurrentImage"
    link: "https://reference.wolfram.com/language/ref/CurrentImage.en.md"
  - 
    title: "CurvatureFlowFilter"
    link: "https://reference.wolfram.com/language/ref/CurvatureFlowFilter.en.md"
  - 
    title: "DeleteSmallComponents"
    link: "https://reference.wolfram.com/language/ref/DeleteSmallComponents.en.md"
  - 
    title: "DynamicImage"
    link: "https://reference.wolfram.com/language/ref/DynamicImage.en.md"
  - 
    title: "FeatureExtract"
    link: "https://reference.wolfram.com/language/ref/FeatureExtract.en.md"
  - 
    title: "FeatureSpacePlot"
    link: "https://reference.wolfram.com/language/ref/FeatureSpacePlot.en.md"
  - 
    title: "FindClusters"
    link: "https://reference.wolfram.com/language/ref/FindClusters.en.md"
  - 
    title: "FindGeometricTransform"
    link: "https://reference.wolfram.com/language/ref/FindGeometricTransform.en.md"
  - 
    title: "HighlightImage"
    link: "https://reference.wolfram.com/language/ref/HighlightImage.en.md"
  - 
    title: "HistogramTransform"
    link: "https://reference.wolfram.com/language/ref/HistogramTransform.en.md"
  - 
    title: "Image3D"
    link: "https://reference.wolfram.com/language/ref/Image3D.en.md"
  - 
    title: "Image3DProjection"
    link: "https://reference.wolfram.com/language/ref/Image3DProjection.en.md"
  - 
    title: "Image3DSlices"
    link: "https://reference.wolfram.com/language/ref/Image3DSlices.en.md"
  - 
    title: "ImageAdjust"
    link: "https://reference.wolfram.com/language/ref/ImageAdjust.en.md"
  - 
    title: "ImageAlign"
    link: "https://reference.wolfram.com/language/ref/ImageAlign.en.md"
  - 
    title: "ImageCorrespondingPoints"
    link: "https://reference.wolfram.com/language/ref/ImageCorrespondingPoints.en.md"
  - 
    title: "ImageDeconvolve"
    link: "https://reference.wolfram.com/language/ref/ImageDeconvolve.en.md"
  - 
    title: "ImageDisplacements"
    link: "https://reference.wolfram.com/language/ref/ImageDisplacements.en.md"
  - 
    title: "ImageFeatureTrack"
    link: "https://reference.wolfram.com/language/ref/ImageFeatureTrack.en.md"
  - 
    title: "ImageFocusCombine"
    link: "https://reference.wolfram.com/language/ref/ImageFocusCombine.en.md"
  - 
    title: "ImageHistogram"
    link: "https://reference.wolfram.com/language/ref/ImageHistogram.en.md"
  - 
    title: "ImageKeypoints"
    link: "https://reference.wolfram.com/language/ref/ImageKeypoints.en.md"
  - 
    title: "ImageMeasurements"
    link: "https://reference.wolfram.com/language/ref/ImageMeasurements.en.md"
  - 
    title: "Import"
    link: "https://reference.wolfram.com/language/ref/Import.en.md"
  - 
    title: "Inpaint"
    link: "https://reference.wolfram.com/language/ref/Inpaint.en.md"
  - 
    title: "ListAnimate"
    link: "https://reference.wolfram.com/language/ref/ListAnimate.en.md"
  - 
    title: "ListContourPlot3D"
    link: "https://reference.wolfram.com/language/ref/ListContourPlot3D.en.md"
  - 
    title: "MeanFilter"
    link: "https://reference.wolfram.com/language/ref/MeanFilter.en.md"
  - 
    title: "NetChain"
    link: "https://reference.wolfram.com/language/ref/NetChain.en.md"
  - 
    title: "NetEncoder"
    link: "https://reference.wolfram.com/language/ref/NetEncoder.en.md"
  - 
    title: "NetGraph"
    link: "https://reference.wolfram.com/language/ref/NetGraph.en.md"
  - 
    title: "NetModel"
    link: "https://reference.wolfram.com/language/ref/NetModel.en.md"
  - 
    title: "NetTrain"
    link: "https://reference.wolfram.com/language/ref/NetTrain.en.md"
  - 
    title: "SelectComponents"
    link: "https://reference.wolfram.com/language/ref/SelectComponents.en.md"
  - 
    title: "TotalVariationFilter"
    link: "https://reference.wolfram.com/language/ref/TotalVariationFilter.en.md"
---
# Image Computation for Microscopy

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](https://reference.wolfram.com/language/guide/CreatingAndImportingImages.en.md)

[`Import`](https://reference.wolfram.com/language/ref/Import.en.md) — import data and metadata from standard formats (TIFF, OME-TIFF, DICOM, ...) and proprietary formats (Leica, Zeiss, Olympus, ...) through [BioFormatsLink](https://github.com/WolframResearch/BioFormatsLink)

[`CurrentImage`](https://reference.wolfram.com/language/ref/CurrentImage.en.md) — capture an image or video in real time from a microscope camera

### Combining Images

[`ImageAlign`](https://reference.wolfram.com/language/ref/ImageAlign.en.md) — align images from a stack or grid of images

* [`Image3D`](https://reference.wolfram.com/language/ref/Image3D.en.md)
* [`ImageFocusCombine`](https://reference.wolfram.com/language/ref/ImageFocusCombine.en.md)
* [`FindGeometricTransform`](https://reference.wolfram.com/language/ref/FindGeometricTransform.en.md)

### [Brightness & Color Enhancement](https://reference.wolfram.com/language/guide/ColorProcessing.en.md)

[`BrightnessEqualize`](https://reference.wolfram.com/language/ref/BrightnessEqualize.en.md) — correct uneven brightness

* [`ImageAdjust`](https://reference.wolfram.com/language/ref/ImageAdjust.en.md)
* [`HistogramTransform`](https://reference.wolfram.com/language/ref/HistogramTransform.en.md)
* [`...`](https://reference.wolfram.com/language/guide/ColorProcessing.en.md)

### [Denoising and Image Restoration](https://reference.wolfram.com/language/guide/ImageRestoration.en.md)

[`ImageDeconvolve`](https://reference.wolfram.com/language/ref/ImageDeconvolve.en.md) — remove blur induced by a point spread function (PSF)

* [`MeanFilter`](https://reference.wolfram.com/language/ref/MeanFilter.en.md)
* [`TotalVariationFilter`](https://reference.wolfram.com/language/ref/TotalVariationFilter.en.md)
* [`CurvatureFlowFilter`](https://reference.wolfram.com/language/ref/CurvatureFlowFilter.en.md)
* [`Inpaint`](https://reference.wolfram.com/language/ref/Inpaint.en.md)
* [`...`](https://reference.wolfram.com/language/guide/ImageRestoration.en.md)

### [Image Properties](https://reference.wolfram.com/language/guide/ImageRepresentation.en.md)

[`ImageMeasurements`](https://reference.wolfram.com/language/ref/ImageMeasurements.en.md) — measure shape and color properties of an image

* [`ImageHistogram`](https://reference.wolfram.com/language/ref/ImageHistogram.en.md)
* [`Image3DProjection`](https://reference.wolfram.com/language/ref/Image3DProjection.en.md)
* [`Image3DSlices`](https://reference.wolfram.com/language/ref/Image3DSlices.en.md)
* [`...`](https://reference.wolfram.com/language/guide/ImageRepresentation.en.md)

### [Segmentation Analysis](https://reference.wolfram.com/language/guide/SegmentationAnalysis.en.md)

[`Binarize`](https://reference.wolfram.com/language/ref/Binarize.en.md) — segmentation by thresholding pixel intensities

[`ClusteringComponents`](https://reference.wolfram.com/language/ref/ClusteringComponents.en.md) — segmentation based on cluster analysis ($k$-means, etc.)

* [`ComponentMeasurements`](https://reference.wolfram.com/language/ref/ComponentMeasurements.en.md)
* [`SelectComponents`](https://reference.wolfram.com/language/ref/SelectComponents.en.md)
* [`DeleteSmallComponents`](https://reference.wolfram.com/language/ref/DeleteSmallComponents.en.md)
* [`...`](https://reference.wolfram.com/language/guide/SegmentationAnalysis.en.md)

### [Feature Extraction & Tracking](https://reference.wolfram.com/language/guide/FeatureDetection.en.md)

[`ImageDisplacements`](https://reference.wolfram.com/language/ref/ImageDisplacements.en.md) — dense tracking of pixels across a sequence of images

* [`ImageFeatureTrack`](https://reference.wolfram.com/language/ref/ImageFeatureTrack.en.md)
* [`ImageKeypoints`](https://reference.wolfram.com/language/ref/ImageKeypoints.en.md)
* [`ImageCorrespondingPoints`](https://reference.wolfram.com/language/ref/ImageCorrespondingPoints.en.md)
* [`...`](https://reference.wolfram.com/language/guide/FeatureDetection.en.md)

### [Classification & Feature Detection](https://reference.wolfram.com/language/guide/ComputerVision.en.md)

[`Classify`](https://reference.wolfram.com/language/ref/Classify.en.md) — categorize images or components

* [`FeatureExtract`](https://reference.wolfram.com/language/ref/FeatureExtract.en.md)
* [`FeatureSpacePlot`](https://reference.wolfram.com/language/ref/FeatureSpacePlot.en.md)
* [`FindClusters`](https://reference.wolfram.com/language/ref/FindClusters.en.md)
* [`...`](https://reference.wolfram.com/language/guide/ComputerVision.en.md)

* [`NetGraph`](https://reference.wolfram.com/language/ref/NetGraph.en.md)
* [`NetChain`](https://reference.wolfram.com/language/ref/NetChain.en.md)
* [`NetTrain`](https://reference.wolfram.com/language/ref/NetTrain.en.md)
* [`NetModel`](https://reference.wolfram.com/language/ref/NetModel.en.md)
* [`NetEncoder`](https://reference.wolfram.com/language/ref/NetEncoder.en.md)
* [`...`](https://reference.wolfram.com/language/guide/NeuralNetworks.en.md)

### [`Visualization`](https://reference.wolfram.com/language/guide/DataVisualization.en.md)

[`DynamicImage`](https://reference.wolfram.com/language/ref/DynamicImage.en.md) — explore an image by zooming and panning

* [`HighlightImage`](https://reference.wolfram.com/language/ref/HighlightImage.en.md)
* [`Colorize`](https://reference.wolfram.com/language/ref/Colorize.en.md)
* [`ListAnimate`](https://reference.wolfram.com/language/ref/ListAnimate.en.md)
* [`ListContourPlot3D`](https://reference.wolfram.com/language/ref/ListContourPlot3D.en.md)
* [`...`](https://reference.wolfram.com/language/guide/DataVisualization.en.md)

## Related Workflow Guides

* [Specific Application Areas](https://reference.wolfram.com/language/workflowguide/SpecificApplicationAreas.en.md)

## Related Guides

* [Image Processing & Analysis](https://reference.wolfram.com/language/guide/ImageProcessing.en.md)
* [Computer Vision](https://reference.wolfram.com/language/guide/ComputerVision.en.md)
* [Machine Learning](https://reference.wolfram.com/language/guide/MachineLearning.en.md)
* [Computational Photography](https://reference.wolfram.com/language/guide/ComputationalPhotography.en.md)