Extensible and Object-oriented System (Eos)
Supplies a New Environment for Image
Analysis of Electron Micrographs of
Macromolecules
Takuo Yasunaga and Takeyuki Wakabayashi
Department of Physics, School of Science, University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo, 113, JAPAN
---- Short Running ----
Extensible system for macromolecular structure analysis
ABSTRACT
To study macromolecular structure by electron microscopy, a highly
extensible and object-oriented system has been developed for image analysis.
This system is named 'Eos' (Extensible and object-oriented system). The system
described here supplies an environment with four types of supports: (i) a group of
small tools for image analysis, (ii) tools for integration of small tools, such as
'Display2', (iii) tools for development, such as 'maketool', and (iv) object-oriented
libraries for development of new tools. Using 'Eos', electron micrographs can be
analysed by small tools and integration tools. Also, 'Eos' can be used to develop
new tools based on new ideas because development tool and object-oriented
libraries are provided. The examples of implemented small tools for image
analysis include three-dimensional reconstruction of objects with helical
symmetry, cluster analysis and contour expression.
INTRODUCTION
The function of macromolecules, such as protein and DNA, is attributable
to their structure. X-ray crystallography and nuclear magnetic resonance
(NMR) are useful to elucidate their structure at atomic level. In the field of
macromolecular structure research, electron microscopy also has helped to
elucidate structure at atomic level (Henderson et al., 1990) and single particle
structure of macromolecules (Frank & Randermacher, 1992; van Heel & Frank,
1981). We have also studied the structure of actin filaments and thin filaments
(Wakabayashi et al., 1975), complexes of actin filaments and myosin
subfragment-1 (Toyoshima & Wakabayashi, 1985) and F1-ATPase structure
(Fujiyama et al., 1990). To study the structure of individual molecules, electron
microscopy is better than X-ray diffraction or NMR, because two-dimensional
projections of specimens can be obtained directly. Electron microscopy is in the
phase of technical development, and new ideas for image analysis should be tried
to obtain new structural information. Therefore, we require an extensible
environment where we can test new ideas for image analysis easily and quickly.
Some useful and powerful tools and packages such as FRODO (Jones,
1978; Jones, 1982), O (Jones, 1991) and X-plor (Bruger, 1992) have been supplied
for the study of structures using X-ray diffraction and NMR. Many packages
such as SPIDER (Frank et al., 1981), Tools for MRC (Moore et al., 1970; DeRosier
and Moore, 1970; Wakabayashi et al., 1975; Amos and Klug, 1975), IMAGIC-5
(van Heel and Keegstra, 1981), SUPRIM (Stoops et al., 1991), and SEMPER
(Saxton et al., 1979) have been also developed for electron microscopy. We have
developed tools required to analyse images of electron micrographs and have
recognised the importance of an environment suitable for developing new tools.
Some packages for general image analysis have been also supplied in the
public domain. The 'Khoros' system (Konstatinides & Rasure, 1994) is one of the
most powerful and extensible systems that can analyse multi-dimensional
images. However, it is difficult to use it, because this system requires a
considerable commitment of resources and expertise.
To overcome such difficulties, we have developed an extensible
environment following the methods used by the 'Khoros' system to achieve
extensibility. Because the essence of extensibility achieved by 'Khoros' is
integration of small smart tools on 'cantata', a visual language, we constructed a
group of small tools and additional tools with which to integrate these together.
Furthermore, we constructed object-oriented libraries to improve extensibility
and productivity.
Thus, the image analysis environment, which is named 'Eos' (Extensible
object-oriented system), has been developed. At present, the system supplies
four types of support to analyse images and to develop new tools: (i) a group of
small tools for image analysis and three-dimensional reconstruction of objects
with helical symmetry, (ii) integration tools such as 'Display2' and examples of
'makefile', (iii) tools for development such as 'maketool', and (iv) object-oriented
libraries for development of new tools. We describe the 'Eos' development
technique, how to use a group of image analysis tools, and how to develop new
analysis tools.
MATERIALS AND METHODS
'Eos' system has been developed on UNIX workstations (HP9000/735,
Hewlett Packard and Domain series, Apollo Inc.). 'Eos' was written in the
ANSI-based C-language using an X-window interface. Originally, graphical
tools such as 'Display2' have been developed on Apollo Domain series because
useful two-dimensional and three-dimensional graphical libraries were available.
X11R5, Xtoolkit, and Motif libraries must be installed on workstations to use
graphical tools, because the tools have been ported to X-Window system (X11R5)
with Motif widgets to achieve general portability.
Manuals are supplied as plain texts and HTML-formatted texts and are
also available on a WWW server (html://tkyemghp.phys.s.u-tokyo.ac.jp/Eos).
Plain and HTML manuals of each tool can be also obtained by using '-h' and '-
html' options, respectively. Each of the tool manuals is almost completed, and
general manuals are now being prepared.
RESULTS
'Eos' system concept
Figure 1 shows the concept of 'Eos', the environment for image analysis
and tool development. 'Eos' supplies four types of support: (i) a group of small
tools for image analysis such as three-dimensional reconstruction of objects with
helical symmetry, (ii) tools for integration of small tools, such as 'Display2' and
examples of 'makefile', (iii) tools for development such as 'maketool', and (iv) a
group of objects, i.e., object-oriented libraries. The two former supports are used
to analyse images of electron micrographs and two latter supports are used to
develop new tools.
The group of small tools and integration tools
Using this group of small tools, 'Eos' users can analyse images of electron
micrographs. 'Eos' supplies more than fifty small tools, such as histogram
normalisation, median filter, low/high/band pass filtering, image correlation,
Fourier and Fourier-Bessel transform, calculating angular distribution in
Fourier space, printing images and contour maps, CTF correction. Cluster
analysis using the 'distance' array and three-dimensional reconstruction of
objects with helical symmetry can also be performed by combination of these
small tools.
Figure 2 shows an example of a three-dimensional reconstruction of
objects with helical symmetry using 'Eos'. Theories and fitting procedures for
three-dimensional reconstruction were developed according to DeRosier and
Moore (1970), Wakabayashi et al. (1975), and Amos and Klug (1975). A flow
chart to obtain a three-dimensional image is shown in Fig. 2a. This indicates
that the reconstruction is performed by a combination of small tools. The
examples of 'Makefile' to integrate these small tools is also shown in Fig. 2b.
Using this 'Makefile', the three-dimensional reconstruction of a filament in Fig.
3a is achieved by simply entering 'make' from a keyboard.
Figure 3 shows the result of image analysis. The three-dimensional
image shown in Fig. 3c was reconstituted from the projected and low pass filtered
image of an atomic model of actin filaments proposed by Lorenz et al. (1993).
The tools of 'Eos' were used to read atomic coordinates from the Protein Data
Bank, obtain the low pass filtered projected densities shown in Fig. 3a from
atomic coordinates and reconstituted three-dimensional densities. In Fig. 3b
the contour maps of two horizontal sections at different z-coordinates are shown.
Because 'Eos' does not support volume rendering or solid modelling yet, the solid
model shown in Fig. 3c was produced by 'xds' supplied by NCSA. To use such
tools, many file-format converters such as mrc2hdf (mrcImage format to HDF by
NCSA), mrc2viff (mrcImage format to Khoros format), mrc2tiff (mrcImage format
to TIFF format), are provided.
Cluster analysis is an important technique in single particle analysis to
determine orientation of particles (van Heel & Frank, 1981). Using 'Eos', we
applied it to actin filaments. Phase residuals (Wakabayashi et al., 1975; Amos
& Klug, 1975) were used as the 'distance' which provides the measurement of the
difference between images. This approach was useful for structural analysis of
actin filaments, because the change of subdomain arrangement could be detected.
The tools for cluster analysis ("llFit", "clustShow", and "arrayClust") can be also
integrated into a 'makefile'.
Both examples show that the integration of small tools by a UNIX 'make'
tool is useful. Updated data can be obtained at the required time. Thus, we
propose an idea for using UNIX 'make' to concatenate or pipeline small tools into
one integrated tool, while 'make' is usually used to create executables from source
codes.
Another integration tool supplied by 'Eos' is 'Display2'. This tool is
suitable for interactive image analysis, e.g. to extract a region of interest. Image
analysis techniques which need an interactive process can be integrated with
'Display2', because this tool has the ability to evoke further small tools.
Development tools and object-oriented libraries
'Eos' supplies development tools such as 'maketool' and object-oriented
libraries to enable easy development and installation of new tools as shown in
Fig. 1.
The 'maketool', which is a shell program, produces a special directory
structure and prototypes of source codes. If a new tool named 'tool' is required to
be developed, 'maketool' supplies prototypes of one header file (tool.h) and five
source files (tool.c, argCheck.c, usage.c, init.c, util.c). Required values and
information can be introduced into source codes interactively by using 'maketool'.
The required information can be obtained from options of tools, a control file or
both, whereas the way to input required data is described in 'Makefile' as shown
in Fig. 2b. One can concentrate on the coding of "tool.c", because it is not
necessary to modify most of the other source files such as "tool.h", "usage.c",
"argCheck.c", or "init.c" if 'maketool' is used. This feature is also useful for
documentation.
Furthermore, the development procedures of new tools are supported by
object-oriented libraries. Tools can be modified or developed in a short time,
because source-format is well-defined. The detailed method for developing a
new tool is described in manuals.
Table 1 shows representative objects supported by 'Eos'. Objects are
classified in three classes, i.e., 'General', 'DataManipulation', and
'DataExpression'. Tools for analysis have been created with combining these
objects. An 'mrcImage' object is important, because it is tightly related to image
data files of MRC format, i.e., CCP4 map format. Because both tools for electron
microscopy by MRC and tools for X-ray crystallography by CCP4 can be applied to
the files with MRC-format, an 'mrcImage' object is useful for comparing three-
dimensional images reconstituted from electron micrographs with atomic
structure obtained by X-ray crystallography.
DISCUSSION
The goal of this system, 'Eos', is to supply an extensible environment for
the image analysis of macromolecular structure. The extensibility described
here suggests both easy integration of small tools in analysing images and easy
development of new tools. We realised or implemented this extensibility by
supplying four types of supports as shown in Fig. 1.
'Eos' supplies examples of 'makefile' for integration of small tools as
shown in Fig. 1 and 2b. We are modifying 'Display2' so as to integrate new
small tools into 'Display2' using a control file to minimise necessary modification
of source codes. When it is completed, 'Display2' will become more convenient.
'Eos' supplies prototypes of source codes using 'maketool' and object-
oriented libraries as shown in Fig. 1. Easy and quick development of new tools
enabled us to rapidly increase the number of supported tools for image analysis in
our laboratory. In the future, modification of development tools such as
'maketool' will be improved by adopting a visual dialogue. Object-oriented
libraries will be also improved by adding new functions and adopting the C++
language.
Acknowledgement
We thanks Drs K. Mitsuoka and S. Nagashima for useful discussions in
developing "Eos" system. This work was supported by the grants: the Grant-in-
Aid for Encouragement of Young Scientists and the grant from the JSPS
Fellowships for Japanese Junior Scientists to T.Y. and the Grant-in-Aid for
Specially Promoted Research from the Ministry of Education, Science and
Culture of Japan to T.W. and the grant from the Biodesign Program, RIKEN to
T.W.
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Figure Legends
Table 1 : This table shows representative objects supplied by 'Eos' system.
Three types of objects are shown.
Figure 1: The concept of 'Eos' system and four types of supports by 'Eos'. Four
shadow squares show four types of supports, i.e., "Group of Small Tools",
"Integration Tools", "Development Tools", and "Group of Objects". When images
are analysed, small tools are integrated using the integration tools. Image
analysis techniques which need interactive processing can be integrated into
'Display2'. When a new tool is developed, a group of prototype source codes is
supplied by a development tool, 'maketool'. Also, the new tool can be developed
using a group of objects. The detailed explanation of "Group of Objects" is
shown in Table 1.
Figure 2: Three-dimensional reconstruction of filaments with helical symmetry as
an example of 'Eos' usage. a. The schematic diagram of the procedure of three-
dimensional reconstruction of specimens with helical symmetry. The left terms
boxed with rectangles indicate 'Eos' objects and the right ones indicate image
files with suffixes. Tools expressed in italic such as 'fft2d ' are supplied by 'Eos'
system. b. An example of makefile for a 'make' tool. Using the UNIX 'make'
tool, each of the small tools is integrated. Each of the data sets is assigned as an
object of a particular type according to a suffix. By using this 'makefile',
updated data can be obtained at the required time.
Figure 3: The results of image analysis using three-dimensional reconstruction of
specimens with helical symmetry. a. A projected image of an actin filament,
which was produced from the atomic model of an actin filament (Lorenz et al.,
1993). This image of a filament is treated as a model of micrographs recorded in
an electron microscope so that the validity of the 'Eos' tools could be tested. b.
Contour maps of horizontal sections at successive z-coordinates of a reconstructed
image of a model actin filament. c. A reconstituted three-dimensional image of a
model actin filament. A three-dimensional image (mrcImage) was transformed
into NCSA-hdf format by 'mrc2hdf' and then the image was displayed with 'xds'
supplied by NCSA.