This lesson is still being designed and assembled (Pre-Alpha version)


Learning Objectives

After completing this lesson, learners should be able to:
  • Examine the values of pixels in an image.


Images are very often composed of pixels. Pixel stands for “picture element”. In 3-D, a pixel is sometimes also called a voxel, which stands for “volume element”. To analyse images it is very important to know how to examine the pixels (voxels) in an image.


graph TD Im("Image") -->|has many| P("Pixel") P -->|has| V("Value") P -->|has| I("Indices") P -->|aka| V("Voxel") P -->|can have| S("Size")


Explore the values, indices (and sizes) of pixels in an image.

Show activity for:

ImageJ GUI

Explore pixel values and indices

  • Open image: xy_8bit__nuclei_noisy_different_intensity.tif
  • Explore different ways to inspect pixel values and indices
  • Check where the lowest pixel indices are in the displayed image: * Most commonly: Upper left corner, which is different to conventional coordinate systems.

Explore pixel sizes

  • Open image: xyz_8bit_calibrated_anisotropic__mri_head.tif
  • Check the pixel sizes (calibration) of this image
  • Explore how image calibration affects spatial measurements, e.g.,
    • Measure the distance between two pixels in the image
    • Measure the size of an image region
  • Appreciate that image calibration might be neccessary, e.g.
    • 3D distance measurements
  • Appreciate that image calibration can be confusing, e.g.
    • not consistently used in image filter parameter specification

Formative assessment

True or false? * The lowest pixel index of a 2D image always is [1,1]. * When looking at a 2D image, the lowest pixel indices are always in the lower left corner.

Follow-up material

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