diff --git a/doc/Doxyfile b/doc/Doxyfile
index 0da9e96..a5d4fd0 100644
--- a/doc/Doxyfile
+++ b/doc/Doxyfile
@@ -655,7 +655,8 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = "."
+INPUT                  = "scripts" \
+                         "src"
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -690,7 +691,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = "pyext"
+EXCLUDE                = ctools* gammalib*
 
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
@@ -705,7 +706,7 @@ EXCLUDE_SYMLINKS       = NO
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = 
+EXCLUDE_PATTERNS       = ctools* gammalib*
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
@@ -713,9 +714,7 @@ EXCLUDE_PATTERNS       =
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
 # AClass::ANamespace, ANamespace::*Test
 
-EXCLUDE_SYMBOLS        = std* \
-                         swig* \
-                         Swig*
+EXCLUDE_SYMBOLS        = std* swig* Swig* ctools* gammalib*
 
 # The EXAMPLE_PATH tag can be used to specify one or more files or
 # directories that contain example code fragments that are included (see
@@ -1363,7 +1362,7 @@ RTF_EXTENSIONS_FILE    =
 # If the GENERATE_MAN tag is set to YES (the default) Doxygen will
 # generate man pages
 
-GENERATE_MAN           = NO
+GENERATE_MAN           = YES
 
 # The MAN_OUTPUT tag is used to specify where the man pages will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
@@ -1722,7 +1721,7 @@ DIRECTORY_GRAPH        = YES
 # HTML_FILE_EXTENSION to xhtml in order to make the SVG files
 # visible in IE 9+ (other browsers do not have this requirement).
 
-DOT_IMAGE_FORMAT       = svg
+DOT_IMAGE_FORMAT       = png
 
 # If DOT_IMAGE_FORMAT is set to svg, then this option can be set to YES to
 # enable generation of interactive SVG images that allow zooming and panning.