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 image - a digital image is a grid of numerical valuesusually measurementsdisplayed according to a lookup table or RGB color values.
- Color images
- Lookup tables (LUTs)
Pixels - pixel is short for picture element. A pixel is the representation of a single value or measurement in a digital image. Digital images are made up of rows and columns of these values, represented on screen as pixels.
Integrating ImageJ with other applications
Introduction to ImageJ
- About ImageJ
- Downloading and installing ImageJ
- Special installation instructions for Windows Vista or Windows 7 users
- Updating ImageJ
Density Calibration - Density calibration involves relating pixel values to real world measurements, such as brightness, elevation, temperature, concentration, etc.
- About the calibration function
- Adding a calibration bar
- Calibration values - where they come from
- Density calibrating images
- Density calibration bug in ImageJ version 1.43o and earlier
- Non-linear calibration
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.
- Choosing which density measurements to make (Set Measurements)
- Creating density profile plots Density profile - A density profile (plot) is a graph of the pixel values along a selected linear path on a digital image. If the pixel values represent elevation, the density profile plot produces a topographic profile.
- Creating histograms Histogram - An image histogram is a graph that shows the number (frequency) of pixels of each possible value in an image. Histograms are also called frequency distribution diagrams.
- Density measurements - definition
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.
- Adding a scale bar
- Definition of spatial calibration (setting scale)
- Finding the image scale
- Setting scale for ground-based (non-nadir) images
- Setting scale using an existing scale bar
- Setting scale using a known distance
- Setting scale using the image resolution
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.
- Adding a scale bar
- Choosing which spatial measurements to make (Set Measurements)
- Definition of spatial measurements
- Making simple spatial measurements
- Measuring a region of interest (ROI)
- Measuring distances
- Measuring in stacks
- Selecting a region of interest (ROI) to measure
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
- Adding and deleting slices in stacks
- Animating stacks (automatic method)
- Animating stacks (manual method)
- Changing image type of a stack
- Choosing the Next Slice
- Choosing the Previous Slice
- Converting a stack to binary images
- Importing a sequence of images as a stack
- Merging stacks
- Reading the slice counter
- Saving stacks
- Setting animation speed
- Stacking images
- Stacking images with different color tables or bit depths
- Unstacking and restacking slices
Montage - a montage is a single image composed of a grid (rows and columns) of smaller images.
Tools and techniques
- ImageJ toolbar
- Scrolling with the Scroll (hand) tool
- Selecting a region of interest (ROI) Region of interest - A region of interest (ROI) consists of a set of pixels you are interested in, defined by making a spatial selection using one or more selection tools and/or defining a range of pixel values using the thresholding technique. In ImageJ, ROIs can be saved, recalled, and manipulated using the ROI Manager under Analyze > Tools > ROI Manager.
- Tiling image windows Tiling - Tiling a set of image windows reduces the scale of the images so that all of the image windows appear on screen at one time. Tiled windows are arranged in rows and columns.
- Zooming with the Zoom tool