Image Processing with ImageJ -- Table of Contents -- Image Processing with ImageJ -- Credits -- About the Authors -- About the Reviewers -- www.PacktPub.com -- Support files, eBooks, discount offers and more -- Why Subscribe? -- Free Access for Packt account holders -- Preface -- What this book covers -- What you need for this book -- Who this book is for -- Conventions -- Reader feedback -- Customer support -- Downloading the example code -- Errata -- Piracy -- Questions -- 1. Getting Started with ImageJ -- ImageJ - history and motivation -- What ImageJ is for (and what it is not for) -- Installing ImageJ -- Windows -- Linux / Mac OS -- First run -- Updating the installation -- Configuration options -- Memory limit increase -- Summary -- 2. Basic Image Processing with ImageJ -- Image reading/writing -- Opening images with a certain format -- Reading raw data -- Online sample images -- Saving images -- Zooming on the image and pixel values -- Color and multichannel images -- 3D and 4D images - stacks and hyperstacks -- Image adjust tools -- Image histogram and window/level parameters -- Thresholding -- Image resizing -- Summary -- 3. Advanced Image Processing with ImageJ -- Selecting regions of your image -- Basic selections - lines, length, and profiles -- Drawing regions of interest over an area -- The ROI manager and the image overlay -- Filters -- Image filtering in the spatial domain -- Edge detection -- The Fourier transform -- Image filtering in the frequency domain -- Particle analysis -- Summary -- 4. ImageJ Macros -- What is an ImageJ macro -- The macro recorder -- Running macros -- Modifying a recorded macro -- More about the macro language - basic syntax and operators -- Variables -- A brief note on debugging a macro -- Control structures -- The for loop -- The while loop -- The if (condition) and if (condition) … else statements.

Defining functions -- Some useful procedures -- Opening an image from a macro -- Finding out how many images are open -- Obtaining the dimensions of an image -- A note on slices, frames, and channels -- Selecting a specific image -- Speeding up a macro -- Adding a GUI to your macro -- The batch mode -- Installing macros for easy access -- Shared macros - the ImageJ macro directory -- Summary -- 5. ImageJ Plugins for Users -- ImageJ plugins -- Installing a plugin -- Some useful plugins -- LOCI Bio-Formats -- Image segmentation -- Auto Threshold and Auto Local Threshold -- The trainable Weka segmentation -- SIOX (Simple Interactive Object Extraction) -- Clustering -- Image registration -- Stackreg -- 3D volume rendering -- Volume Viewer -- Other utilities -- MosaicJ -- FigureJ -- Study anonymization -- FIJI (Fiji Is Not ImageJ) -- Summary -- 6. ImageJ Plugins for Developers -- A sample plugin -- The PlugInFilter interface -- Adding a GUI to your plugin -- The ImageJ plugin API -- Setting up ImageJ under the Eclipse IDE -- Our first Eclipse ImageJ plugin -- Sharing your plugin -- Using external libraries -- Summary -- Index.