\HeaderA{EBImage}{Package overview}{EBImage}
\keyword{package}{EBImage}
\begin{Description}\relax
\code{EBImage} is an image processing and analysis package for R. Its primary
goal is to enable automated analysis of large sets of images such as those
obtained in high throughput automated microscopy.

The package uses the \code{ImageMagick} library for image I/O operations and
some image processing methods. The \code{GTK} library is used for displaying images
using \code{display}.

\code{EBImage} relies on the \code{Image} object to store and process images
but also works on multi-dimensional arrays.
\end{Description}
\begin{Section}{Package content}
Image methods
\Itemize{
\item \code{Image}
\item \code{as.Image}, \code{is.Image}
\item \code{colorMode}, \code{imageData}
\item \code{getNumberOfFrames}
}

Image I/O, display
\Itemize{
\item \code{readImage}, \code{writeImage}
\item \code{display}, \code{animate}
\item \code{image}
}

Spatial transform
\Itemize{
\item \code{resize}, \code{flip}, \code{flop}
\item \code{rotate}, \code{translate}
}

Image segmentation, objects manipulation
\Itemize{
\item \code{thresh}, \code{bwlabel}
\item \code{watershed}, \code{propagate}
\item \code{ocontour}
\item \code{paintObjects}, \code{rmObjects}, \code{reenumerate}
}

Image enhancement, filtering
\Itemize{
\item \code{normalize}
\item \code{filter2}, \code{blur}, \code{gblur}
\item \code{equalize}
}

Morphological operations
\Itemize{
\item \code{makeBrush}
\item \code{erode}, \code{dilate}, \code{opening}, \code{closing}
\item \code{distmap}
\item \code{floodFill}, \code{fillHull}
}

Colorspace manipulation
\Itemize{  
\item \code{rgbImage}, \code{channel}
}

Image stacking, combining, tiling
\Itemize{ 
\item \code{stackObjects}
\item \code{combine}
\item \code{tile}, \code{untile}
}

Drawing on images
\Itemize{
\item \code{drawfont}, \code{drawtext}
}

Features extraction
\Itemize{
\item \code{getFeatures}
\item \code{hullFeatures}
\item \code{edgeProfile}, \code{edgeFeatures}
\item \code{moments}, \code{cmoments}, \code{smoments}, \code{rmoments}
\item \code{haralickFeatures}, \code{haralickMatrix}
\item \code{zernikeMoments}
}

Deprecated
\Itemize{
\item \code{frameDist}, \code{matchObjects}
\item \code{stopIfNotImage}
\item \code{morphKern}, \code{mkbox}, \code{mkball}
\item \code{header}, \code{assert}
\item \code{chooseImage}
\item \code{resample}, \code{sharpen}, \code{umask}, \code{modulate}
\item \code{negate}, \code{affinet}, \code{normalize2}, \code{noise}
\item \code{mediansmooth}, \code{cgamma}, \code{enhance}, \code{denoise}
\item \code{contrast}, \code{despeckle}, \code{edge}, \code{segment} 
\item \code{cthresh}, \code{athresh}
\item \code{channelMix}
}
\end{Section}
\begin{Section}{Authors}
Oleg Sklyar, \email{osklyar@ebi.ac.uk}, Copyright 2005-2007

Gregoire Pau, \email{gpau@ebi.ac.uk}

Wolfgang Huber, \email{huber@ebi.ac.uk}

Mike Smith, \email{msmith@ebi.ac.uk}

\begin{alltt}
  European Bioinformatics Institute
  European Molecular Biology Laboratory
  Wellcome Trust Genome Campus
  Hinxton 
  Cambridge CB10 1SD
  UK
\end{alltt}

The code of \code{\LinkA{propagate}{propagate}} is based on the \code{CellProfiler} 
with permission granted to distribute this particular part under LGPL, the 
corresponding copyright (Jones, Carpenter) applies.

The source code is released under \code{LGPL} (see the \code{LICENSE} 
file in the package root for the complete license wording). \code{ImageMagick} 
and \code{GTK} used from the package are distributed separately by the 
respective copyright holders.

This library is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the
License, or (at your option) any later version. This library is distributed
in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

See the GNU Lesser General Public License for more details. For LGPL license 
wording see \url{http://www.gnu.org/licenses/lgpl.html}
\end{Section}
\begin{Examples}
\begin{ExampleCode}
  example(readImage)
  example(display)
  example(rotate)
  example(propagate)
\end{ExampleCode}
\end{Examples}

