"Serial section reconstruction" software can refer to several different
methodologies.
The following listing is for software for "contour or structure" oriented
reconstructions. That is, software which can align sections, then extract
(usually manually) 3D structural information (such as contour outlines) from
the aligned images. It tries not to list reconstruction software
for volume rendering or simple stacking (alignment) of sections.
Neither does it list software which merely segments an object from
a volume by thresholding or surface definition (such as the marching cubes
algorithm). "Contour or structure" oriented reconstructions are useful when
the data has gaps between sections or the desired information can not be
segmented algorithmically in a practical manner.
Disclaimer: With the exception of the Sterecon site,
I am not familiar with the working of much of the software
presented here. These are merely pointers to some
software that may be of use or interest.
.
- STERECON
STERECON (STEREo CONtour Reconstruction System
for Microscopy Data) from Wadsworth Lab's
Resource for the Visualization of Biological Complexity (RVBC)
is a software package for making contour-based 3-D reconstructions
from microscope images. It is distringuished by its ability
to use stereo views. Sterecon software is
available for non-commercial use.
Platform: SGI only
- VoxBlast
VoxBlast from
Vaytek Inc.
, Fairfield, Iowa,
is a commercial software package that contains an
module for "Slice tracing" which appears to do
contouring.
Platform: Windows, Mac & Some Unix
- Micro3D
Micro3D from
NeSys Laboratory,
Dept. of Anatomy, Univ. of Oslo, Oslo, Norway
is "adapted to the use of data from serial microtome sections"
Platform: SGI & maybe other Unix
- Reconstruct
Reconstruct from
The Laboratory of Synapse Structure and Function,
Boston Univ., Boston, MA. can
"Identify, measure, outline and reconstruct objects from serially-sectioned images"
Platform: Windows
- SYNU
SYNUview/OpenSynu from
The National Center for Microscopy and Imaging Research
(NCMIR) has a facility for making contour-based 3-D
reconstructions from microscope images. The Resource's software "SYNUview"
is available from that site.
"Synu is a collection of programs for manipulation and
visual presentation of scientific data. Synu works with
polygon meshes, stacks of contour lines, or three-dimensional
volumes from confocal Z-series, tomography, or simulations."
Platform: Systems with X Window and OpenGL.
- Image Pro Plus
Image Pro Plus from
Media Cybernetics
is a commercial image analysis package which reportedly contains a
module for automatic extraction of image features including contours.
This software was used in the
Visable Embryo
project at the
Electronic Visualization Laboratory University of Illinois at Chicago
Platform: Windows
- IMOD
IMOD from the
Boulder Laboratory for 3-Dimensional Fine Structure
is a free
software package, which is a "set of image processing, modeling and
display programs used for 3D reconstruction of EM serial sections,
tomographic sections and optical sections developed by Jim Kremer and
David Mastronarde."
Platform: Linux & Windows
- Nuages
Nuages from
PRISME
is a free software package for 3D reconstruction
from parallel cross-sectional data written by Bernhard Geiger.
Platform: Most Unix
- Montage
Montage is a free software package from the
University of Pennsylvania,Anatomy Dept.
that was one of the earliest computer based
serial-section reconstruction packages. It includes component programs
for data entry from digitizer, 3D reconstruction and display, and
surface area/volume analysis.
Platform: PC & Linux
- BioQuant
BioQuant is a commercial hardware/software package from
BioMetrics / BioQuant Image Analysis Corp.
that can do measurement and automatic
outlining of structures on serial sections. It appears to
only be sold with hardware for frame grabbing direct from a video camera.
Platform: PC (Windows)
- Volume4D PRO
Volume4D PRO from ScienceGL
Quincy, MA can do measurements within volumes and may be able to do
contour tracing.
- 3D-DOCTOR
3D-DOCTOR is a commercial software package from
Able Software
that can do measurement and alignment
of structures on serial sections. I am uncertain whether
it can do interactive contour tracing or just automatic
object segmentation.
Platform: PC (Windows)
- NeuroModeller
NeuroModeller is a free software package from
Cornell University Division of Neurosurgery that can do some
automatic visualization and manipulation of surface iso-contours. It
might work on registered em files?
Platform: PC (Windows)
- 3D-TOP
3D-TOP is a software package by Andres Kriete of the Univ. Giessen that
can do most types of serial section reconstruction and visualization. A
demo software with limited capacity is available via the Internet.
Platform: SGI
- NIH Image
Some people have reported using this free
software package for serial section reconstruction but it appears
to have been used mainly for alignment not contour extraction?
Platform: Mac
- MeX
MeX from
Alicona Imaging
is commercial software for creating and analyzing digital elevation models
from stereoscopic scanning electron microscope images.
Platform: Windows, Linux (Other Unix??)
- Insight Segmentation and Registration Toolkit (ITK)
The Insight Segmentation and Registration Toolkit from the
National Library of Medicine ITK Project
is "an open-source software toolkit that employs leading-edge
segmentation and registration algorithms in
two, three, and more dimensions". It does not designed for tracing
but may be usefull for image processing prior to tracing.
Platform: Unix & Windows
- SURFdriver
SURFdriver is a commercial software package for 3-D reconstruction. It
can create 3D models from contour tracings. (Web site appears broken 2007)
Platform: MS-Windows & Mac.
Broken/Obsolete links for Products which May No Longer Exist?
- analySIS
analySIS from
Soft Imaging System GmbH
, Münster, Germany
is a commercial software package that contains an
optional module "Stereom" which can calculate quantitative elevation
maps and measurements on the basis of two images acquired from
different points of view. It does not appear to do contour
tracing however. (Product may no longer exist in 2007?)
Platform: Windows.
- ROSS
(Mar 2007 -- unable to locate software site)
ROSS (Reconstruction Of Serial Sections) from the NASA Ames Center for
Bioinformatics is a restricted (US research labs
only) free software package for performing 3D serial-section
reconstruction and visualization from microscopy images. Typically, it
is used for reconstructing biological tissue that has been sectioned
either physically (as in light or electron microscopy) or optically (as
in confocal microscopy or MR and CT imaging).
ROSS contains modules for Mosaicing, Contouring, Registration, and Visualization
Platform: SGI
- C_Images 3D
C_Images 3D from
Foster Findlay Associates
is a commercial software package which contains a
development tool kit of software for the analysis of three
dimensional images. "C_Images 3D provides full three dimensional
processing and analysis". Can perform three-dimensional measurements,
3D distance transforms, volume fusion, user defined filtering and
automatic '3D body' detection.
No mention of stereo analysis capability or serial section ability.
(Product no longer existd in 2007?)
Platform: PC and UNIX
- MacStereology
Link currently broken (Mar. 2001)
MacStereology is free demo
package designed to make measurements of images and to
make 3-D reconstructions. The boundaries of objects of interest can be
drawn by hand on the tablet or traced automatically on a image.
Parameters such as area, perimeter and centre of gravity are obtained.
3-D reconstructions can be created. Certain features, especially the
saving of data, have been disabled in the demo.
A commercial firm: Ranfurley MicroSystems, 20 St Omer Rd, Cowley, Oxford
OX4 3HB. email: cmpowell@rmplc.co.uk phone:(44) 01865 777486 that
reportedly sold a full version may have disappeared.
Platform: Macintosh
- ImageVolumes
Company may have disappeared? (Sept. 2001)
ImageVolumes from
Minnesota Datametrics Corporation is a commercial software system
that does three-dimensional
reconstruction, visualization and quantification from volume data.
Input can be digitized images, or two-dimensional
data that describe contours and points. A 3D graphical editing module, ContourEdit, lets you edit
and align serial section contours. There are other modules for
measurement and display.
Platform: SGI
