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About digital images

Modern microscope systems transform optical images into digital images, which are arrays of pixels.

The optical image is formed by photons. These photons, after passing through the optical system, are collected by a detector, which converts the light into an electrical signal. The electrical signal from a particular area of the field of view is in turn converted into a numerical pixel value (intensity or gray value). This process is repeated over the whole field of view to produce an array of pixel values that (we hope) accurately represents the optical image.

Imaging software displays this array of pixel values so that we can interpret the data. It does this by converting each numerical value into a particular color on the computer screen.

After images are acquired, software can be used:

  • to display pixel data in different ways, to help the viewer understand the results (visualization and rendering)
  • to alter the pixel values to make the image clearer in some way (image processing)
  • to gather information from images (image analysis)

Introduction to fluorescence image analysis by Peter Bankhead

Useful software

ImageJ is the software of choice for many image analysis and processing tasks.

It is free, has a large user base and is being actively developed and improved.

Fiji is our recommended distribution of ImageJ, because it includes many useful enhancements.

Getting started with ImageJ and Fiji


Brightfield correction by Gabriel Landini

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