Pixels

Learning Objectives

After completing this lesson, learners should be able to:

• Examine the values of pixels in an image.

Motivation

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.

Concept

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")

Activity

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

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

We recommend reading these modules next:

• Image display

Learn more: