The Image Processing Cookbook, 4th Edition by John Russ

Author:John Russ [Russ, John]
Language: eng
Format: azw3
Publisher: UNKNOWN
Published: 2017-04-20T04:00:00+00:00

The FIJI (“Fiji Is Just ImageJ”) download ( https:// ji.sc) includes with ImageJ a set of prepackaged plugins, most of them intended for use on 3D stacks of images from a confocal microscope, and applicable to the study of biological tissue. However, some of these plugins provide speci c routines not present in ImageJ that implement functions illustrated in this text. Examples include:

Anisotropic diffusion and bilateral lters

Kuwahara lter for edge sharpening

Several deconvolution methods

Additional algorithms for automatic threshold determination

EDM-based watershed segmentation

Analysis of skeletons by removal of terminal branches

Registration (alignment) of multiple images, intended for a 3D data set but also generally

applicable to focus stacks

The documentation for each plugin is provided by the individual authors, usually on separate websites or by reference to publications that show an example of use, and is highly variable and often minimal.

Appendix E - Image-Pro Plus This appendix summarizes a basic set of commands that implement the functions illustrated in the text, using Media Cybernetics Image-Pro Plus <http://www.mediacy.com/index.aspx? page=IPP>. The program is typically sold in conjunction with a light microscope, and includes interface software for microscope control and image capture. It runs only under Windows. The notes correspond to version 7.0. In order to maintain continuity with older versions and any automatic sequences originally written for them, there are some options and menu selections that are redundant, providing more than one way to access the same function, and some less accurate computations using older algorithms and implementations (for example integer-based) have been retained. In addition to the menu selections described here, the program has scripting and automation capability, some provisions for 3D and time-sequence image handling, and manual editing and annotation features. A full manual is available on-line at <ftp://ftp.mediacy.com/tech/ PDF/IPPReference_7.0.pdf>, which includes extensive information on the data export, automation macro language, and hardware control portions of the package.

Basic image handling Images of various types (gray scale, RGB, 8, 12 or 16 bit, in a variety of storage le types) are read and saved and displayed using the usual commands under the File> menu (also selectable from the tool bar). Each image is displayed in its own window, and the frontmost window with the highlighted name is the one operated on by the processing and measurement routines. Edit>Undo can be used to revert up to the four most recent processing operations.

Images may be converted from one format to another by selecting Edit>Convert To. The result is shown in a separate window and is treated as a new image. Many of the processing functions described below have the option to either replace values in the current image or to create a new image in a separate window.

The Toolbar has tools for enlarging the image on the screen, reading point coordinates and pixel values, selecting regions, measuring point-to-point distances, etc., as well as image annotation tools. Measure>Histogram shows the image histogram, which can be saved to a disk le (e.g., for reading with Excel). For a color image, the color box selects the channel represented.

Most of the functions listed below operate only within a selection, called an AOI (Area of Interest), if one has been de ned.

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