See the file BUILDING for building instructions.  The setup program makes 
configuration files based on machine-specific details in the "machines" 
directory.

Upon unpacking the source, you will find the following directories:

autodoc         Autodoc files for programs using PIP package for input
clip		Source for Command Line Image Processing
com		Command files, mostly used by copytomocoms for tomography
ctfplotter      Source for ctfplotter program
dist		Files for installation and distribution
Etomo           eTomo package tree
Etomo/doc       Program documentation files
Etomo/scripts   Has an eTomo testing script
Etomo/src       Top of source tree
Etomo/src/etomo All java source is under here
  .../comscript Command script classes
  .../logic     
  .../process   Process-running classes
  .../storage   File-related classes
  .../type      Classes to handle specific data items
  .../ui/swing  Dialog classes
  .../uitest    Classes for the UI testing
  .../util      Utility functions
Etomo/src/images  Has icons
flib		Fortran program source tree
flib/beadtrack	Source for bead tracker program
flib/blend	Source for montage blending program and montage reducer
flib/distort	Source for distortion-finding program
flib/graphics	Source for several programs using line graphics
flib/image	Source for many programs that do not use models or graphics
flib/man	Master directory for man pages of Fortran programs
flib/model	Source for many programs that use IMOD models
flib/ndasda	Source for nda, sda, and mtk spatial analysis programs
flib/subrs	Top of source tree for Fortran libraries
  .../blas      Source for blas routines needed by lapack
  .../compat    Source for compatibility routines where needed
  .../dtrigs	Source for cosd, sind, etc. functions for Linux (libdtrigs)
  .../graphics	Source for graphics subroutines (libdnmncar)
  .../hvem	Source for miscellaneous subroutines developed here
  .../ifftsub	Source for FFT subroutines  (libifft - no longer used)
  .../imsubs	Source for basic image I/O routines  (libim)
  .../imsubs2	Source for other image manipulation routines  (libim)
  .../lapack    Source for subset of lapack needed by ctfplotter
  .../linetrack	Source for line tracker subroutines
  .../model	Source for model-related subroutines  (libwmod)	
  .../piecesubs	Source for routines that work with piece coordinates  (libhvem)
  .../randm	Source for Linux replacement for RAN function  (librandm)
  .../smallmodel  Derived source for library that has a small model (libsmlmod)
  .../statsubs	Source for statistical subroutines
  .../xfsubs	Source for routines that work with transformations
flib/tilt	Source for back-projection program
flib/tilt/fbplib  Source for library of routines for fast back-projection
flib/tiltalign	Source for tilt alignmnet program
html		All html documents and files that they link to
html/3dmodHelp  Help files for 3dmod
html/3dmodimages Images for introduction to 3dmod
html/ctfHelp    Help files for ctfplotter
html/etomoImages Images for etomo tutorial
html/joinImages  Images for join tutorial
html/libdoc     Framework files for library documentation
html/midasHelp  Help files for midas
3dmod		Source for 3dmod program
imodutil	Source for utility programs for working with IMOD models
include		Include files for IMOD programs
libcfft         Source for C version of FFT library
libcfshr        Source for library of utilities shared with Fortran
libdiaqt        Source for Qt dialog and utility library
libiimod        Source for IMOD image library
libimod         Source for IMOD model library
libmesh         Source for meshing library
libwarp         Source for warping library, includes natural neighbor 
                       interpolation and Delaunay triangulation code
machines	Machine-specific files included by setup script
manpages	Master source for man pages of C programs, in nroff format
midas		Source for midas program
mrc		Source for various programs manipulating MRC image files
plugs		Source tree for imod plugins
plugs/analysistools  Source for Andrew Noske's analysis tools plugin
plugs/beadfix	   Source for old version of bead fixer plugin used to test build
plugs/beadhelper   Source for Noske's bead helper plugin
plugs/drawingtools Source for Noske's drawing tools plugin
plugs/interpolator Source for Noske's interpolator plugin
plugs/namewizard   Source for Noske's namewizard plugin
plugs/noskecommon  Source for common files for Noske's plugins
plugs/stereology   Source for Noske's stereology plugin
processchunks   Source for processchunks program
pysrc           Python scripts
qtassist        Source for imodqtassist program
raptor          Source for RAPTOR
scripts		Shell scripts
sendevent       Source for imodsendevent program
sourcedoc       Source for sourcedoc program (Qt-based)
sysdep          System dependent files needed for builds
sysdep/mac      Files for OS X build - not currently needed
sysdep/win      Files for Windows build - Tiff-related files and manifests


After doing a "make" and default "make install", you will have:

buildlib	Newly built but uninstalled libraries, needed to make programs
man		Top directory for man pages (contains a cat1 and cat5)
html/man	Html versions of man pages
html/libhelp    Processed library documentation files
html/plughelp   Copies of plugin help files, needed for inclusion in IMOD.qch
bin		Installation directory for executable programs and scripts
lib		Installation directory for libraries (old 32-bit on SGI)
lib/imodplug	Installation directory for imod plugins
pylib           Installation directory for Python modules

Other files in top directory:
BUILDING        Details for building IMOD on all platforms
History         Has the complete history of changes
installqtlib    Does post-install copying of libraries and startup files
Makefile        Master Makefile for build
packMacApps     For a Mac install, puts Qt programs into .app directories
setup           Starting script for configuring for build
setup2          Real configure script; setup runs dos2unix on it in Cygwin
vcimod.dsw      Workspace for midas, 3dmod, imodsendevent in Visual C++