Eos is an electron microscope image analysis software developed and published since 1996 by Takeyuki Wakabayashi and Takuo Yasunaga. Originally was a collection of programs of 50 or so. Then by software development with students, it is an integrated environment that is composed of program of about 400 on the electron microscope image processing, currently.
Overview of Eos
Eos is named using first letters of "Extensible Object-oriented System" after the goddess of the dawn Eos in Greek mythology. We have the hope that many programs will be developed from here. We think there is a strong transmission for many of the commands and rapid development, and the development of effective programs for the user through integration. At present, it is referred to as a platform that such program environment is established, but it was called "environment" because it was not a word popular development at that time.
1996 - 2011
Eos system supplies four types of codes. We provid two of them for Developers, other two for Users. The support for Developers of the former are Object-oriented library and Prototype Source code, the support for Users of the latter are Small Tools of viable and Integration program that integrates them. Integration program is one that is provided as part of the command as Display2, and Makefile( In the future, integrating to PIONE with GUI) for make.
We added the class of Experts to categories such as the Users and the Developers. One fo the Experts is the layer that can be programmed in the scripting language level and electron microscope image processing. In addition, it was running by integrating of make through shell script initially, after that the time has change when computing environment itself become cloud and cooperative computing systems, so we decided to achieve the transformation to a platform to help them. It is developing, however we aim to the Enhancement of the layers of the scripting language and the level including those related to the display, such as a GUI.
And we describe Loadmap about the direction of future development.
Supports for Users
For users to perform an electron microscope image processing, Eos provides a program of more than 400 in 2012, and Integrated program of their such as for Electron tomography and Single particle analysis.
Idea of Eos is near to that of UNIX. On UNIX, Commands (ls/cat/grep/sed ... ) specializes in the work of each specific are provided. They are integrated by shell script, and perform large-scale works. On Eos, basically small tools are integrated by Integration Programs, and perform large-scale works (Single particle analysis or Electron tomography ...). Please refer to the page for details of each general image processing for Pre-processing and Post-processing, commands for 3D Reconstruction, Correction of EM images, List of command, and Functional Order of Commands.
In addition, we are developing the tools to run through a browser GUI from the commands of each.
On Eos, large-scale works as Electron tomography are performed by this Integration Tools. And, we provide Integration Commands that can use Object-oriented library as API. The former is integration of commands, and the latter is integration of API from library.
Provided of Makefile
We provide basic Makefile for Correction of EM images, Electron tomography, 3D Reconstruction(Estimation of projection angle using reference, Random conical tilt, by Common lines), 3D Reconstruction by spiral symmetry etc... . These Makefile are improved by each users (here called experts) for each analysis. Eos provide basic Makefile mainly.
Provided of PIONE
Currently, We aim to be able to perform in a distributed environment, and we are developing a new integrated program (PIONE) at a rapid pace. Already, the β version have been published, transplantation of image processing part is in progress.
It uses Object-oriented library and Commands as API, and it provide Integration Program such as Display2, ctfDisplay, molvie, and smolet. we are developing Display2 aiming to ImageJ, and smolet aiming to etomo and 3dmod.
Support for Developers
Another main purpose of Eos is the rapid development of the required program. In particular, with the aim of researchers who are not professional development can try and apply the needed algorithm as soon as possible, we developed in a form that summarizes the development of programs to it in 1996. Because it was a time that specification has not been fixed with still developing is Object-oriented language as C++, summarizes the knowledge of that time, and we have developed C++ and sell script(including Awk). Currently, there is old specifications or problems as of today by reviewing. We have a refactored of them each continuously、and proceed to cover the whole by the script language of Object-oriented system (e.g. ruby). In addition, the part of parallel processing developed by pvm initially become parallel processing distributed processing of different architectures for 15 years, therefore we are considering a mechanism that corresponds to it.
It is a set of API group for image processing. It has been created with the policy for exchanging data by the transfer of the structure. Refer to Object-oriented library、API list or Functional order of API about API7s details.
It provides the Prototype Source code of C language. We provide Prototype Source code for input and output arguments and their communications by using the define file that is called OptionControlFile.