Image Volumes
The ImageVolumes system for the Silicon Graphics IRIS workstation provides
a complete software environment for three-dimensional (3D) reconstruction,
visualization and quantification of volumetric data. Input can be
digitized gray scale images, or two-dimensional (2D) graphics data that
describe contours and points. You can interactively process either form of
data to produce sophisticated 3D shaded surface models. An image
processing module, Image, lets you enhance and analyze serial section gray
scale images using several different classes of functions, including
radiometric, filtering, algebraic, geometric and morphologic. A 3D
graphical editing module, ContourEdit, lets you edit and align serial
section contours and point data taken from digitizing tablets or
microscope stage digitizers such as the MD2 Microscope Digitizer from
Minnesota Datametrics. The 3D display and analysis modules, Display and
Metrics, make full use of the visualization features of the IRIS
workstations including their surface materials and light source modeling
capabilities and their fast hidden surface removal and polygon rendering.
Most importantly, you can make measurements on 3D models such as
distances, numbers of objects, surface areas and volumes. In addition,
ImageVolumes now includes new advanced analytical tools for quantification
and classification of 3D models, such as the distance field and 3D model
intersection tool, DField.
Overview
You control actions in ImageVolumes using an interactive, screen oriented
DataFlow Manager. By simply clicking the mouse on one or more icons you
define the sequence of operations on your data and the results to be
displayed and stored. At each step of the process the DataFlow Manager
assists you in the selection of appropriate input and output data files.
The major programs within ImageVolumes are:
- Image - An interactive image processor that operates on digitized gray
scale images.
- ContourEdit - A screen oriented 3D database editor.
- Cubes - A polygon and voxel generator that processes your serial section
data and stores a 3D geometry database of surface polygons and voxel
densities.
- Display - Displays your reconstruction with user defined surface materials
properties, Phong shading and multiple light sources.
- Metrics - A volumetric analysis program for measuring sizes and numbers of
objects and their surface areas and volumes.
- DField - Computes distance fields of 3D surface models and quantifies
intersections between 3D surface models. Distance fields can also be
used to interpolate iso-surfaces between two 3D models.
Image Processing
Image is an interactive 2D image display and processing program. Images
can be displayed singly, as movie loops or as a mosaic. You can choose
from among radiometric, algebraic, geometric, filtering , morphological
and graphical overlay functions. The program supports region-of-interest
processing and can be run using scripts or macros that are learned by the
software during your processing operations. Major image processing
categories in Image include:
- Radiometric operations - Gray level scaling, histogram normalization,
histogram equalization, binary level slice, piecewise linear
transformation, local adaptive histogram equalization (LAHE) and local
adaptive histogram normalization (Wallis).
- Algebraic operations - Add, subtract, multiply, divide, square root and
logarithm of gray scale images.
- Geometric operations - Image translation, rotation and scaling. A
registration feature allows interactive alignment of pairs of images.
- Filtering operations - Smoothing and median filtering. Kirsch, Laplace,
Roberts, sharpening, sigma and Sobel edge detection operators. Special
line detect filter for enhancing thin fibrous structures.
- Morphological operators - Area fill, dilate, erode, boundary track and
medial axis operators for delineating boundaries, identifying objects and
creating overlay masks to be used for region-of-interest operations during
radiometric and filtering operations.
Interactive Graphics Editing
ContourEdit lets you edit graphics data in the form of points, lines and
closed contours. Data can come from a variety of sources including a
digitizing tablet, boundaries of objects extracted from images by the
Image program or the MD2 Microscope Digitizer from Minnesota Datametrics.
You can view your data interactively in 3D from any vantage point using
orthographic or perspective projection. Individual vertices, points, lines
or contours can be selected using hardware picking and then visually
translated, rotated or scaled and saved in their new position. Vertices
can be deleted from or added to line and contour elements. Lines and
contours can be copied or created as interpolations of adjacent lines or
contours. Set operations are one of the most powerful features of
ContourEdit. Elements can be added to or removed from named sets of
elements and each set treated as a single geometric object. Set name
information is preserved in the database and individual sets can be
written to their own disk files.
Isosurface Extraction and 3D Rendering
Cubes analyzes your serial section data, be it digitized gray scale images
or processed contour and point data, and writes a 3D geometry file
containing a winged-edge, linked list of surface polygons and vertex
normal vectors. Voxel values can also be extracted from image data and
saved in the geometry file.
The Display program renders your 3D model using sophisticated graphics
techniques:
- Ambient, diffuse, specular, transparency and emissive properties by simply
choosing a material from a supplied library of materials - or design your
own materials.
- Multiple, colored light sources.
- Phong shading for seamless rendering of surfaces.
- Smoothing of surfaces.
- Interactive translation, rotation, scaling and spinning of 3D models.
- Automated animation of rotation sequences with frame-by-frame screen
capture to disk files.
Volumetric Analysis
The Metrics program allows you to measure the numbers of objects, surface
areas and volumes of all or a portion of a 3D model using a bounding box.
The bounding box can also be used to create cutaway views.
DField computes distance fields of 3D surface models and intersections
between 3D surface models.
Utility Functions
The full-featured version of ImageVolumes is supplied with a number of
utilities for image format conversion, 3D geometry file format conversion
and for capturing screen images to disk in tagged-image-file-format
(TIFF). Image conversions include TIFF, PCX, sample-scanline and PIC.
Geometry file conversions include AutoCAD DXF.