ImageJ Index

ImageJ Concepts, Skills, & Techniques

  • Bit depth and color images
    Bit depth - The bit depth of an image is the number of binary digits (bits) required to describe the value of each pixel. ImageJ can work with grayscale images having bit depths from 1 bit (binary images, showing just black or white pixels) to 32 bits per pixel. Color images consist of three separate channels representing the additive primary colors red, green, and blue. Color image bit depths range from 8-bitss (indexed color) to 24-bit RGB color images.
  • Correcting contrast of true and false color images
  • Creating color images from stacks
  • Creating false color images
    False color - Color images in which bands representing wavelengths other than red, green, and blue are assigned to the red, green, and blue color channels. False color images are used to emphasize and identify specific types of features.
  • Creating true color images
    True color - Color images that approximate what would be seen with the human eye, usually by assigning images of or close to the red, green, and blue wavelengths to the red, green and blue color channels.
  • Interpreting false color images
  • Landsat Thematic Mapper bands
  • Memory and color images
  • Multispectral and hyperspectral imaging
    Multispectral imaging - Multispectral imaging involves creating images at several different discrete wavelengths, and hyperspectral imaging involves capturing a scene in a series of contiguous wavelength bands, ranging from hundreds to thousands of wavelengths.
  • Primary colors
    Primary colors - The additive primary colorsRed, Green, and Blueare the colors (wavelengths) of light that mix to produce the visible spectrum. They are Red, Green, and Blue. The subtractive primary colorsCyan, Magenta, and Yelloware used when producing color using inks or dyes.
  • Reading RGB pixel values
  • Separating color channels
    Color separation - Color separation involves converting a single multiband color image into a set of separate grayscale images, where each image represents one color channel or wavelength.

Digital images
Digital image - a digital image is a grid of numerical valuesusually measurementsdisplayed according to a lookup table or RGB color values.

Integrating ImageJ with other applications
Introduction to ImageJ

Density Calibration - Density calibration involves relating pixel values to real world measurements, such as brightness, elevation, temperature, concentration, etc.
Density Measurements - Density measurements include statistical measures of pixel values, such as mean, median, and mode. If an image is density calibrated in some units, the measurements are given in calibrated units. If a region of interest (ROI) has been selected, only the pixels in the ROI is measured. If no ROI is defined, all of the pixel values in the image are considered.
Spatial Calibration ("Setting Scale") - Spatial calibration involves relating image distances, areas, and volumes in pixels to real world distances, areas, and volumes. Also referred to as setting scale.
Spatial Measurements - Spatial measurements include distances, areas, and volumes. If an image is uncalibrated, these are given in pixels, square pixels, and cubic pixels. If an image is spatially calibrated in some units, the measurements are given in units, square units, and cubic units. If a region of interest (ROI) has been selected, only the ROI is measured. If no ROI is defined, the entire image is measured.

Stack - an image window containing two or more digital images as layers or slices. A normal image window has two dimensionswidth and height; a stack window has three dimensionswidth, height, and slices. Different slices typically represent differences or changes in time, space, wavelength, focal plane, or feature type.
Definition Stack basics Uses of stacks
Tools and techniques

ImageJ Resources