Difference between revisions of "Main Page"

Revision as of 04:08, 17 July 2014 (view source) Kinoshita (Talk | contribs) (→‎Single particle analysis　) ← Older edit		Revision as of 04:16, 17 July 2014 (view source) Kinoshita (Talk | contribs) (→‎Electron tomography) Newer edit →
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	==== Interpretation of 3D reconstruction ====		==== Interpretation of 3D reconstruction ====
	Last, we must perform segmentation of 3D objects to interpret them.  Thus we must use computer-aided visualization tools.		Last, we must perform segmentation of 3D objects to interpret them.  Thus we must use computer-aided visualization tools.
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		+	==== Averaging of Subtomograms ====
	=== Notes ===		=== Notes ===

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Revision as of 04:16, 17 July 2014

Welcome to Eospedia

We started the new manual site of Eos for only few people at 05 Nov. 2010. We would like to summarize knowledges about Eos.

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.

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.

Installation

Necessary environment

Download

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

Integration 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.

Eos tutorial　

How to set Eos environment　

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

• 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.

• Eos Commands

Image format on Eos　

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

• [Image Format|Image Format]]
• [Image format transform|Image format transform]]

Simple image processing using Eos　

Simple image processing and analysis can be performed here.

• Simple 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.

• CTF Correction

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.

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

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

Alignment

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

3D reconstruction

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

Problems of 3D reconstruction

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

Notes

　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 oder 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.

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

EM Image Processing

Montage

CTF Collection

Alignment of 3D objects

Alignment of a series of images

Electron Microscopy

We here describe electron microscopy.

Electron source

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

Lens

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.

FAQ and TIPS

FAQ

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

Eos TIPS

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

Eos around TIPS

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

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

External link

• Eospedia.jp
• Eospedia.en
• Eos SourceForge
• Yasunaga Lab.
• Kyutech, Dept. of Bioscience and Bioinformatics
• Kyutech. School of Computer Science and Systems Engineering
• Kyushu Institute of Technology(Kyutech)

• Software Tools For Molecular Microscopy
• EM Software on EMDataBank

How to use mediawiki

• Configuration Settings
• FAQ
• mediawiki-announce