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Welcome to Eospedia

We started the new manual site of Eos for only few people at 05 Nov. 2010. And we started the operation of Eospedia closed β version of the laboratory. In August 2012, we opened as the head family of the home page of the electron microscope image processing system Eos here.

We would like to summarize extensive knowledges as description and algorithm of the command about Eos. Also We will summarize here in the same way for the PIONE (developing since 2012) and VEM/WITs (developing since 2013). In addition, we would like to operate as a site that is possible to learn including an electron microscope image processing, the basics of the various image processing here.

We are developing Eos on Eos@sourceforge, PIONE on PIONE@github. We would like to expand the information that summarizes them here. In the future, we are considering also be independent of the university. Try and take a look at this related sites If you are interested in any of the development and use of these. The philosophy of wiki is not "how do us prevent mistakes" but "how do us improve it". Therefore we are glad, if you write freely your know-how and knowledge without afraid to make mistakes (Of course, incoherence is out of the question.).

Old Eos pages are here.

Now this Eospedia is under construction. Eospedia.ja has also opend here. Japanese version of Eospedia has more information than this Eospedia in English.

In addition, there is a forum and mailing list for Eos. If you want to know how to use the Eos: eos-users@ If you are interested in the development of in Eos: eos-developers@ If you are able to help write the document of Eos: eos-document@ If you can cooperate, we are glad.

We opened "Eos User Group"[1] on the facebook futher. We would like to spread using this.

Please contact Yasunaga[2] for more information.

Over-all view of the system that we are now developing (Eos/PIONE/Zephyr & WITs/VEM system)

We are currently developing a new system, namely "Eos/PIONE/Zephyr & WITs/VEM system", which would provide a total solution for image acquisition, processing and analysis of electron microscopic data by taking care of a series of necessary workflows in the analysis. The system has integrated each system (Eos, PIONE, Zephyr & WITs and VEM) that were developed for specific stages in the EM data analysis, and therefore can be termed as "Systems of System". But below we start by describing the summary and purposes of each system.

You can find a summary description of the integrated system in Eos/PIONE/Zephyr/WITs/VEM system (Under construction)

Beginner's Guid

What is Eos ?

We here describe what is Eos.

How to use Eos Commands

We here describe commands of Eos by CUI.

How to use Eos by Makefile

We here describe how to integrate commands using make

List of command

We here show all of commands Eos supplies.

Functional order of Eos command list

We here show functional order of Eos commands.


Required Environment


We here describe how to download Eos. We are currently developing a Eos at SourceForge.

How to install Eos

We here describe how to install Eos.

Installation of PIONE

We here describe how to install a new process flow control system, PIONE. PIONE has been developed on "github".

Eos reference

Integrated commands supplied by Eos

We here describe integration commands supplied by Eos, one of the support Eos supplies.

Integration comannd : PIONE

We here describe PIONE that is provided as an integrated environment that corresponds to the cloud environment and distributed environment by Eos.

Eos tutorial 

How to set Eos environment 

At first, we explain how to install Eos simplily. The details are described in Eos Installation.

How to use commands of Eos 

We explain how to use Eos commands. In details, please refer to the Eos Commands. Eos perform image processing and analysis with CUI, normally, although some interactive tools have GUI. In the near-future, each command has GUI on a browser by javascript.

Image format on Eos 

Image formats in Eos and how to transform image format from other general image formats are explained here.

Simple image processing using Eos 

Simple image processing and analysis can be performed here.

Tutorial List

Here are Makefile and PIONE for Small Tools or several Image Processing.

CTF Correction

Electron micrographs were greatly modified in contrast due to how to take them. Here we show the correction methods of CTF.

Single particle analysis 

This is a tutorial section of single particle analysis. Here we show the single particle analysis with reference. Actually, we must choose the 3D Reconstruction methods considering the situations.

Concept of Single particle analysis

Particle picking

At first, we pick particles from electron micrographs. Here, the manual picking method is shown, although automatic methods are also proposed.

Classification of 2D images

Next, we classify 2D-images following their shape and so average them per cluster to improve the ratio of signal to noise.

Estimation of projection angle using reference

Third, we determine the projection angle of each particle in the case of the presence of reference images, although the determination methods of projection angles are also proposed without reference.

Estimation of projection angle without using reference

As another way, we show the method of determining the projection angle of each particle in the case of not using reference images. Method of Common Line Search by Common Line is general.

3D Reconstruction: Backprojecdtion

Forth, we reconstruct 3D objects from 2D images, especially Backprojection.

Visualization tools

FInally, we interpret 3D objects reconstructed from 2D images using visualization tools.

Electron Tomography

Electron Tomography is one of the powerful techniques to solive 3D objects such as whole cell, cytoskeleton in cell, and protein structure with polymorphism. It reconstruct 3D objects from tilt-series images of the same photo field.

The overview of Electron Tomography

Electron Tomography can supply us 3D objects from tilt-series of 2D images of the same field. Here we explain the overview.

Image Correction

Fist, we must correct CTF (Contrast Transfer Function) becuase the 2D images are taken with larger defocusing values.

Rough Alignment

Next, we align 2D images roughly using correlation between each image.

Fine Alignment

Third, we estimate the tilt-axis position and angles.

3D Reconstruction

Fourth, we reconstruct 3D image from a set of tilt-series images.

Problems of Electron Tomography image

 We must pay attention of misleading blurring due to missing area, which is generated from the limitation of projection angles.

Interpretation of 3D Reconstruction

Last, we must perform segmentation of 3D objects to interpret them. Thus we must use computer-aided visualization tools.

Averaging of Subtomograms

Tomogram images of cryo-microscopy include a lot of noise, thus it is required the averaging of the particles have the same structure.


 This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.

Developers' Guide of Eos

Eos System Architecture

For Eos System Developers

Eos System Commands

Eos development under Sourceforge

We here show a flow of development of Eos under Sourceforge: 1. create clone from Sourceforge, develop a new tool or object and finally register them into Sourceforge.

Development of small tools

How to create a small tool

How to create Small Tools(Command Group) is described.

Introduction of small tools

We introduce some simple examples of Small Tools(Command Group).

How to create API

How to carete Object-oriented library (API) is described。

API list

We show a list of Object-oriented library (API).

Functional order of API

We here show functionl oder of API (Object-oriented libraries) supplied by Eos.

How to create integration commands

We describe how to develop integration commands.

Integration by Makefile

Here how to integrate commands using Makefile are shown。Furthreore, Visualmake supply simple and easy GUI (Graphical User Interface).

Integration by PIONE

We here show how to integrate commands using PIONE, which is a rule-based process definition and work under distributed computing system.

PIONE tutorial

Here is the tutorial how to use PIONE.

PIONE tutorial-PNML

Here, describe how to design process definition document by using PIONE.

Integration by bash

bash etc.

Integration by integration commands

We here describe how to integrate commands by Display2, smolet, Eos etc. programed with Tcl/Tk, ctfDisplay etc. programed with Ruby/Tk,molvie etc. programmed by C-language.

Image Processing and Image Analysis

General Image Processing

Summarizing about the general image processing here.

Simple Image Processing

Tutorial on simple image processing using the Eos has been published.

Input of image and Lens

Before performing image processing using a computer, you should keep in mind about the input device that digitize images.


True image: f(x,y) is degraded due to the method of Input of image and performance of the Lens.


To convert analog images to digital images, it is important that discretize the space by decomposing. This step is called Sampling.


First, in digital image process the operation that expresses density values ​​within certain number of bits (Optical density) is required. This operation is called quantization(AD convert).

Noise reduction

In order to deal the image including a lot of noise, knowing well the nature of the noise is important.


This is an image processing method with the primary purpose of eliminating the noise in the image. By understanding well the nature of the noise, the noise can be reduced properly.

Edge extraction

This is an important step in order to understand the shape of the object, but it is also a very difficult step.


This is the process of isolating the background and the signal, and extracting the representative point and the skeletal. And it is the start process of the analysis and image processing.

Image processing using the Fourier Space

Image processing using the Kernel of the Real space

Image processing using the Mathematical morphology

EM Image Processing

Summarizing about the EM image processing here.

Montage and Panorama image

This is how to combine multiple images obtained by photographing the different regions (However, the set of image overlapping portion thereof ), to create an image of a large area.

CTF Collection

EM image has received the image modulation in principle. It is the image processing to correct the image modulation.

Alignment of 3D objects

It is a method for removing noise by averaging the three-dimensional image with each other.

Alignment of a series of images

It is a method for reconstructing a three-dimensional image by combining the position of the image between the serial sections.

3D Reconstruction

3D Reconstruction is a technique of reconstructing a three-dimensional image from a two-dimensional image.

Central Slice Theorem

 Why can the internal structure be proved by the projected image? It is Central Slice Theorem that proves it.

Fourier method



Electron Microscope

We here describe electron microscopy.

Electron gun

We here describe an electron source of electron microscope, a gun.


We here explain the mechanism of lens and optics, especially TEM (Transmission Electron Microscopy).

Contrast of TEM

We here explain what is contrast of TEM.

Contrast of SEM

We here explain what is contrast of SEM.

Contrast of STEM

We here explain what is contrast of STEM.

Electron cryo-microscopy

We here explain what is electron cryo-microscopy

FAQ of electron microscopy

We here answer the FAQ.

TIPS of electron microscopy

We here collect EM TIPS.

The future of Eos

 The future of Eos (Loadmap) is shown here.



We here plan to collenct FAQ(Frequenty asked question).


We here plan to collect TIPS in using Eos and processing/analyzing/intepreting images.

TIPS around software related to Eos

We here plan to collect useful TIPs around Eos. If you have some comments, please send me.

TIPS around software related to LINUX

Why we have been developing Eos/PIONE ?

Comparing the date when Eos was born, 1996, many types of software for electron micrographs have been developed and used for more users and biologist. Nonetheless, we also ask ourselves the reason why we have been developing and maintenance Eos. We will note Why Eos by Yasunaga.

Eos User Group

We plan to create Eos User Group and discuss the current and the future of Eos on the sourceforge or facebook. Please access them.

About a symbol mark of Eos

Now we plan to make a symbol mark of Eos. If you have some ideas about Eos symbol, please send us yours.

If you want to know how to use mediawiki, please refer to User's Guid

Tools and Sites related to Eos

Programming languages

Related workflow(PIONE)

Petri Net

Action description

Log file

Documentation tools

External link

How to use mediawiki