| category Bioinformatics  | tag ImageJ  Plot 

ImageJ introduction

ImageJ is a public domain Java image processing program inspired by NIH Image for the Macintosh. It runs, either as an online applet or as a downloadable application, on any computer with a Java 1.4 or later virtual machine. Downloadable distributions are available for Windows, Mac OS, Mac OS X and Linux.


By default, the DPI in the JPEG header is set to 72. For a higher value, use a unit of “inch” in the Analyze -> Set Scale dialog (requires v1.40 or later). For example, setting “Distance in Pixels” to 300, “Known Distance” to 1 and “Unit of Length” to “inch” will set the DPI to 300.

Note that ImageJ does not read or write the resolution for JPG files, only that of TIFFs.

Color Spaces

  • Grayscale: The simplest color representation has no color at all, just black, white, and shades of gray.
  • RGB: red, green, and blue. RGB is an additive color model — the desired color is created by adding together different amounts of red, green, and blue light.
  • CMYK: Another way to add color to an image is to subtract it. In subtractive color models, each channel represents a pigment absorbing a certain color. CMYK color represents a common color printing process, with cyan, magenta, yellow, and black inks (the K stands for “key”).

Use this submenu to determine the type of the active image or to convert it to another type.

  • 8-bit. Converts to 8-bit grayscale.
  • 8-bit Color. Converts to 8-bit indexed color using Heckbert’s median-cut color quantization algorithm.
  • RGB Color. Converts to 32-bit RGB color.

Image -> Type -> 8-bit will convert color to grayscale.


Image -> Crop

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