+\subsection{File - Properties}
+Properties of image files include
+\begin{itemize}\itemsep=0pt
+ \item Whether the image is real or complex valued
+ \item Numeric statistics
+ \item Image file labels
+\end{itemize}
+
+\subsection{File - Export}\index{Image export}
+This command allows for exporting image files to a standard
+graphics file format. This is helpful when you want to take an
+image and import it into another application. The current
+\helprefn{intensity scale}{intensityscale} is used when exporting
+the file. The support file formats are:
+
+\begin{twocollist}
+\twocolitem{\textbf{PNG}}{Portable Network Graphics format. This uses 8-bits or
+256 shades of gray.}
+\twocolitem{\textbf{PNG-16}}{This is a 16-bit version of PNG which allows for
+65536 shades of gray.}
+\twocolitem{\textbf{PGM}}{Portable Graymap format. This is a common format used on
+UNIX systems.}
+\twocolitem{\textbf{PGM}}{ASCII version of PGM.}
+\end{twocollist}
+
+
+\subsection{View}\label{intensityscale}
+These options are for change the intensity scale for viewing the image.
+They do not change the image data.
+\subsubsection{Set}
+This command brings up a dialog box that allows you to set the lower
+and upper intensities to display.
+
+\subsubsection{Auto}
+This command brings up a dialog box that allows \ctsim\ to automatically
+make an intensity scale. The options that \ctsim\ needs to make this
+automatic scale are:
+
+\begin{twocollist}
+\twocolitem{\textbf{Center}}{This sets the center of the intensity scale. Currently,
+\ctsim\ allows you to use either the mean, mode, or median of the image
+as the center of the intensity scale.}
+
+\twocolitem{\textbf{Width}}{This sets the half-width of the intensity scale. The width
+is specified as a ratio of the standard deviation.}
+\end{twocollist}
+
+As an example, if \texttt{median} is selected as the center and
+\texttt{0.5} is selected as the width, the the minimum intensity will
+be \texttt{median - 0.5 x standard deviation} and the maximum will be
+\texttt{median + 0.5 x standard deviation}.
+
+\subsubsection{Full}
+This resets the intensity scale to the full scale of the image.
+
+\subsection{Image}
+These commands create a new image based upon the current image,
+and for some commands, also a comparison image.
+
+\subsubsection{Add, Subtract, Multiply, Divide}
+These are simple arithmetic operations. \ctsim\ will display a dialog
+box showing all of the currently opened image files that are the
+same size of the active image. After selecting a compatible image,
+\ctsim\ will perform the arithmetic operation on the two images and
+make a new result image.
+
+\subsubsection{Image Size}
+This command will generate a new window with the current image scaled to
+any size. Currently, \texttt{bilinear} interpolation provides the best
+image quality.
+
+\subsubsection{3-D Conversion}
+Generates a 3-dimensional view of the current phantom. This view can be
+rotated in three dimensions. The left and right arrow control the z-axis
+rotation, the up and down arrows control the x-axis rotation. The y-axis
+rotation is controlled by the \texttt{T} and \texttt{Y} keys. Other options
+include:
+
+\begin{itemize}
+\item Surface plot
+\item Smooth shading
+\item Lighting on or off
+\item Color scale
+\end{itemize}
+
+\subsection{Filter}\index{Image filter}
+These commands filter and modify the image.
+
+\subsubsection{Arithmetic}
+These are simple arithmetic functions that should be self explanatory.
+
+\subsubsection{Frequency Based}
+This commands allow the Fourier and inverse Fourier transformations of
+images. By default, the transformations will automatically convert
+images from Fourier to natural order as expected. For example, \texttt{2-D FFT}
+will transform the points into natural order after the Fourier transform.
+Similarly the inverse, \texttt{2-D IFFT}, will reorder the points from
+natural order to Fourier order before applying the inverse Fourier transformation.
+
+As you would expect, images that undergo frequency filtering will be complex-valued
+images. Normally, only the real component is shown by \ctsim. However, \ctsim\ does
+have options for converting a complex-valued image into a real-valued image via
+the \texttt{Magnitude} and \texttt{Phase} filtering commands.
+
+\subsection{Analyze}
+These commands are used for analyzing an image.
+
+\subsubsection{Plotting}
+The commands plot rows and columns of images. There are also commands
+that perform FFT and IFFT transformations prior to plotting.
+
+\subsubsection{Image Comparison}
+This command performs statistical comparisons between two images. An option
+also exists for generating a difference image from the two input images.
+
+There are also commands for plotting rows and columns from two images on
+a single plot. This is quite helpful when comparing a phantom to a reconstruction.