Difference between revisions of "Main Page"

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	== '''Welcome to Eospedia''' ==		== '''Welcome to Eospedia''' ==
−	We started the new manual site of Eos for only few people at 05 Nov. 2010.	+	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.
−	We would like to summarize knowledges about [[Eos]].	+	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 [https://sourceforge.jp/projects/eos/ Eos@sourceforge], [[PIONE]] on [https://github.com/pione 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 [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos_old here].		Old Eos pages are [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos_old here].
	Now this Eospedia is under construction. Eospedia.ja has also opend [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ here]. Japanese version of Eospedia has more information than this Eospedia in English.		Now this Eospedia is under construction. Eospedia.ja has also opend [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ 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"[https://www.facebook.com/EosUserGroup] on the facebook futher. We would like to spread using this.
		+
		+	Please contact Yasunaga[mailto:yasunaga@bio.kyutech.ac.jp] 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''' ==		=='''Beginner's Guid''' ==
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	We here describe what is Eos.		We here describe what is Eos.
−	=== [[Command|How to use Eos Commands]]	+	=== [[Command|How to use Eos Commands]] ===
	We here describe commands of Eos by CUI.		We here describe commands of Eos by CUI.
−	===[[Makefile|How to use Eos by Makefile]]	+	===[[Makefile|How to use Eos by Makefile]] ===
	We here describe how to integrate commands using [[make]]		We here describe how to integrate commands using [[make]]
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	We here show all of commands Eos supplies.		We here show all of commands Eos supplies.
−	===[[Functional Order of Commands]Functional order of Eos command list]	+	===[[Functional Order of Commands|Functional order of Eos command list]] ===
	We here show functional order of Eos commands.		We here show functional order of Eos commands.
	== '''Installation'''==		== '''Installation'''==
		+	=== [[Required Environment]] ===
		+
	=== [[Download|Download]] ===		=== [[Download|Download]] ===
−	1. tarball [http://www.yasunaga-lab.bio.kyutech.ac.jp/ja/reserach/eos/eos-download-sites/]	+	We here describe how to download Eos. We are currently developing a Eos at SourceForge.
−	2. git from SourceFoge [http://sourceforge.jp/projects/eos/]	+
−	3. (PIONE) github or gem	+
−	3.1 gem (ruby)	+
−	$ gem install pione	+
−		+
−	3.2 git from github	+
−	$ git clone https://github.com/pione/pione.git	+
	=== [[Installation|How to install Eos]] ===		=== [[Installation|How to install Eos]] ===
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	== '''Eos reference''' ==		== '''Eos reference''' ==
−	=== [Integration Commands|Integration commands supplied by Eos]] ===	+	=== [[Integration Commands | Integrated commands supplied by Eos]] ===
	We here describe integration commands supplied by Eos, one of the '''support''' Eos supplies.		We here describe integration commands supplied by Eos, one of the '''support''' Eos supplies.
	=== Integration comannd : [[PIONE]]===		=== Integration comannd : [[PIONE]]===
−	We here describe 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'''　==		== '''Eos tutorial'''　==
	=== How to set Eos environment　===		=== How to set Eos environment　===
−	最初にEosのインストール方法を簡単に説明します。詳細は、[[インストール方法|Eosのインストール方法の詳細]]をご覧下さい。	+	At first, we explain how to install Eos simplily. The details are described in [[Eos installation|Eos Installation]].
−	* [[Eosのインストール|Eosのインストール方法]]	+	* [[Eos installation|Eos Installation]]
−	=== Eosでのコマンドの取り扱い　===	+	=== How to use commands of Eos　===
−	Eosのコマンドの簡単な使い方を説明します。詳細は、[[コマンド|コマンドの詳細]]をご覧下さい。Eosでは、基本はCUIを使ったコマンドの実行により画像処理を進めます。その結果は、ファイルとして保存され、その内容を確認することが出来ます。	+	We explain how to use Eos commands. In details, please refer to the [[Commands|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のコマンド|Eosのコマンド]]	+	* [[Commands |Eos Commands]]
−	=== Eosでの画像の取り扱い　===	+	=== [[Image format on Eos]]　===
−	Eosで取り扱うことのできる画像フォーマットと一般的な画像フォーマットからの変換方法を示します。	+	Image formats in Eos and how to transform image format from other general image formats are explained here.
−	* [[画像フォーマット変換|画像フォーマットの変換]]	+	* [[Image Format|Image Format]]
		+	* [[Image format transform|Image format transform]]
−	=== Eosを使った簡単な画像処理　===	+	=== Simple image processing using Eos　===
−	Eosを使った簡単な画像処理を実行してもらいます。	+	Simple image processing and analysis can be performed here.
−	* [[簡単な画像処理|簡単な２次元画像処理]]	+	* [[Simple Image Processing|Simple Image Processing]]
−	=== CTF画像補正　===	+	=== [[Tutorial List]] ===
−	電子顕微鏡画像では、その撮影方法に由来して、コントラストが大きく変調を受けています。ここでは、その画像のコントラストの変調を補正する方法を示します。	+	Here are [[Makefile]] and [[PIONE]] for [[Small Tools]] or several [[Image Processing]].
−	* [[CTF補正|CTFの補正]]	+
−	=== 単粒子解析の基礎　===	+	=== CTF Correction ===
−	ここでは、単粒子解析の基礎を行います。実際の単粒子解析は、粒子の形やその対称性などを使って探索方法や3次元再構成法を切り替えることができます。	+	Electron micrographs were greatly modified in contrast due to how to take them.  Here we show the correction methods of CTF.
		+	* [[CTF Correction|CTF Correction]]
−	==== [[単粒子解析]]の概要 ====	+	=== Single particle analysis　===
−	単粒子解析の概要を示します。	+	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.
−	==== [[粒子抽出|粒子の抽出]] ====	+	==== Concept of [[Single particle analysis]] ====
−	まず、単粒子を抽出します。ここでは、手動で切り出す方法を示します。自動で切り出す方法も各種提案されています。	+
−	==== [[２次元画像の分類|２次元画像の分類]] ====	+	==== [[Particle picking|Particle picking]] ====
−	２次元画像を分類して、ＳＮ比を上げます。	+	At first, we pick particles from electron micrographs.  Here, the manual picking method is shown, although automatic methods are also proposed.
−	==== [[参照付投影角度決定|参照像があるときの投影角の決定方法]] ====	+	==== [[Classification of 2D images|Classification of 2D images]] ====
−	参照像があるときの投影角の決定方法を説明します。参照像としては、単なる球や楕円体などとすることもあり得ます。参照像がない場合の構造解析法も別途存在しています。	+	Next, we classify 2D-images following their shape and so average them per cluster to improve the ratio of signal to noise.
−	==== [[３次元再構成・逆投影|３次元再構成・逆投影法]] ====	+	==== [[Estimation of projection angle using reference|Estimation of projection angle using reference]] ====
−	3次元再構成自身を解説します。	+	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.
−	==== [[可視化ツール|可視化ツール]] ====	+	==== [[Estimation of projection angle without using reference]] ====
−	できあがった三次元像を可視化するためのツールを紹介します。	+	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: Backprojection|3D Reconstruction: Backprojecdtion]] ====
		+	Forth, we reconstruct 3D objects from 2D images, especially Backprojection.
−	=== [[電子線トモグラフィー]] ===	+	==== [[Visualization tools|Visualization tools]] ====
−	電子線トモグラフィーとは、同一視野の連続傾斜像から、その視野の３次元画像を再構成する方法です。細胞内の構造や構造多型性をもつタンパク質の構造解析に有効な方法です。	+	FInally, we interpret 3D objects reconstructed from 2D images using visualization tools.
−	==== [[電子線トモグラフィー]]の概要 ====	+	=== [[Electron Tomography]] ===
−	電子線トモグラフィー法は、同一視野の傾斜シリーズ画像のセットから３次元像を再構成する方法です。ここではその概要を述べます。	+	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.
−	==== [[画像の補正]] ====	+	==== The overview of [[Electron Tomography]] ====
−	傾斜画像では、視野全体がアンダーフォーカスとなるように、通常の電子顕微鏡撮影よりも大きなデフォカース値をとる場合が多いです。その場合、LaB6などの電子銃では第一トーンリングより外側の情報がほとんど無いために、CTF補正等は必要ありませんが、電界放出銃を利用した場合には、場合によっては間違った情報を与える場合があるので注意が必要です。	+	Electron Tomography can supply us 3D objects from tilt-series of 2D images of the same field.  Here we explain the overview.
−	==== ラフ・アラインメント ====	+	==== [[Image Correction]] ====
−	傾斜画像の中心付近の画像の相関から、それぞれの傾斜画像の大まかな位置を合わせます。	+	Fist, we must correct [[CTF]] (Contrast Transfer Function) becuase the 2D images are taken with larger defocusing values.
−	==== アラインメント ====	+	==== [[Rough Alignment]] ====
−	傾斜画像の軸の位置、角度を出来る限り一致させます。	+	Next, we align 2D images roughly using correlation between each image.
−	==== ３次元再構成 ====	+	==== [[Fine Alignment]] ====
−	２次元画像のセットから３次元画像を再構成します。	+	Third, we estimate the tilt-axis position and angles.
−	==== 画像のもつ問題点 ====	+	==== [[3D Reconstruction]]  ====
−	全方位からの投影像を得られないために、ミッシングエリアとよばれる情報がない領域があります。そのため、方向依存でのボケを生じます。	+	Fourth, we reconstruct 3D image from a set of tilt-series images.
−		+
−	==== 画像の解釈 ====	+
−	また、多様な構造を含むため、３次元画像から興味あるセグメントを切り出すなどの作業が必要です。そのための支援ソフトウェアが必要です。	+
−		+
−	===備考 ===	+
−	上記のチュートリアル・ページは、2012/09/10-11 単粒子解析Workshopでの資料を元に作成したものです。	+
−	今後もこのサイトを充実させ、ワークショップ等で利用していきたいと考えています。	+
		+	==== [[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.
		+	=== Notes ===
		+	This tutorial pages were created with refer to the documents used single particle workshop on 2012/09/10-11.
	== '''Developers' Guide of Eos''' ==		== '''Developers' Guide of Eos''' ==
−	=== [[For Eos System Developers]] ===
	=== [[Eos System Architecture]] ===		=== [[Eos System Architecture]] ===
		+
		+	=== [[For Eos System Developers]] ===
		+
	=== [[Eos System Commands]] ===		=== [[Eos System Commands]] ===
−	== Eosにおける開発（開発者向け） ==
−	=== [[Eosの構造|Eosの構造]] ===
−	Eosの構造(Architecture）について述べます。
−	=== [[Eosの開発|Eosの開発]]===	+	=== [[Eos development under Sourceforge|Eos development under Sourceforge]]===
−	SourceForgeからクローンを作成し、localで新規ツールなどを開発した後、SourceForgeに登録するまでの流れを示します。	+	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.
−	=== [[ツールの開発]] ===	+	=== [[Development of small tools]] ===
−	==== [[ツールの作り方]] ====	+	==== [[How to create a small tool]] ====
−	Eosの上での[[Small Tools]]([[コマンド群]])の作り方について述べます。	+	How to create [[Small Tools]]([[Command Group]]) is described.
−	==== [[簡単なプログラム例]] ====	+	==== [[Introduction of small tools]] ====
−	Eosの上での[[Small Tools]]([[コマンド群]])の簡単なプログラム例について述べます。	+	We introduce some simple examples of [[Small Tools]]([[Command Group]]).
−	=== [[ライブラリ（API）の作り方]]===	+	=== [[How to create API]]===
−	Eosの上での[[オブジェクト指向型ライブラリ]]（[[API]]）の作り方について述べます。	+	How to carete [[Object-oriented library]] ([[API]]) is described。
−	=== [[ライブラリ(API)一覧]]===	+	=== [[API list]]===
−	Eosの上での[[オブジェクト指向型ライブラリ]]（[[API]]）の一覧です。	+	We show a list of [[Object-oriented library]] ([[API]]).
−	=== [[機能別ライブラリ(API)一覧]]===	+	=== [[Functional order of API]]===
−	Eosの上での機能別に分類された[[オブジェクト指向型ライブラリ]]（[[API]]）の一覧です。	+	We here show functionl oder of API ([[Object-oriented libraries]]) supplied by Eos.
−	=== [[統合コマンドの作り方]]===	+	=== [[How to create integration commands]]===
−	統合コマンドの作り方を示します。	+	We describe how to develop integration commands.
−	==== [[Makefileによる統合]] ====	+	==== [[Integration by Makefile]] ====
−	[[Makefile]]を用いた統合方法について示します。[[Visualmake]]は自動的に簡易型のGUIを提供します。	+	Here how to integrate commands using [[Makefile]] are shown。Furthreore, [[Visualmake]] supply simple and easy GUI (Graphical User Interface).
−	==== [[PIONEによる統合]]  ====	+	==== [[Integration by PIONE]]  ====
−	分散環境（クラウド環境）に対応したプロセス定義書[[PIONE]]を用いた統合方法について示します。	+	We here show how to integrate commands using [[PIONE]], which is a rule-based process definition and work under distributed computing system.
−	==== [[bashによる統合]] ====	+	==== [[PIONE tutorial]] ====
−	bashなどのスクリプト言語による統合方法について示します。	+	Here is the tutorial how to use [[PIONE]].
−	==== [[統合コマンドによる統合]] ====	+	==== [[PIONE tutorial-PNML]] ====
−	[[Display2]], [[smolet]], [[Eos]]などのTcl/Tk型の統合コマンドによる統合, [[ctfDisplay]]等のRuby型の統合コマンドによる統合，[[molvie]]などのＣ言語型の統合コマンドによる統合、などの各種方法について示します。	+	Here, describe how to design process definition document by using [[PIONE]].
−	== [[画像処理]] ==	+	==== [[Integration by bash]] ====
−	=== [[画像処理一般]] ===	+	bash etc.
−	ここでは画像処理一般に関する話をまとめています。	+
−	=== [[電子顕微鏡画像処理]] ===	+	==== [[Integration by integration commands]] ====
−	電子顕微鏡画像処理に関する話をまとめています。	+	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.
−	==== [[モンタージュ]] ====	+	== [[Image Processing]] and [[Image Analysis]] ==
		+	=== [[General Image Processing]] ===
		+	Summarizing about the general image processing here.
−	==== [[CTF補正]] ====	+	==== [[Simple Image Processing]]====
		+	Tutorial on simple image processing using the Eos has been published.
−	==== [[３次元画像の位置合わせ]] ====	+	==== [[Input of image]] and [[Lens]] ====
		+	Before performing image processing using a computer, you should keep in mind about the input device that digitize images.
−	==== [[シリアル画像の位置合わせ]] ====	+	==== [[CTF]], [[PSF]] and [[MTF]] ====
		+	True image: f(x,y) is degraded due to the method of [[Input of image]] and performance of the [[Lens]].
−	== [[電子顕微鏡]] ==	+	==== [[Sampling]] ====
−	ここでは電子顕微鏡に関する基礎、FAQ、TIPSをまとめておきます。	+	To convert analog images to digital images, it is important that discretize the space by decomposing. This step is called Sampling.
−	=== [[電子銃]]===	+	==== [[Quantization]] ====
−	電子顕微鏡の電子線源である電子銃についての解説です。	+	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).
−	=== [[電子レンズ]]===	+	==== [[Noise reduction]] ====
−	透過電子顕微鏡の光学系、及び、レンズの仕組みに関する解説です。	+	In order to deal the image including a lot of noise, knowing well the nature of the noise is important.
−	=== [[透過型電子顕微鏡のコントラスト]]===	+	===== [[Smoothing]] =====
−	透過型電子顕微鏡(TEM)がつくるコントラストに関する解説です。	+	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.
−	=== [[走査型透過電子顕微鏡のコントラスト]]===	+	==== [[Edge extraction]] ====
−	走査型透過電子顕微鏡(STEM)がつくるコントラストに関する解説です。	+	This is an important step in order to understand the shape of the object, but it is also a very difficult step.
−	=== [[走査型電子顕微鏡のコントラスト]] ===	+	==== [[Binarization]] ====
−	走査型電子顕微鏡(SEM)がつくるコントラストに関する解説です。	+	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.
−	=== [[クライオ電子顕微鏡法]] ===	+	==== Image processing using the [[Fourier Space]] ====
−	クライオ電子顕微鏡法に関する解説です。	+
−	=== [[電子顕微鏡のFAQ]] ===	+	==== Image processing using the [[Kernel]] of  the Real space ====
−	電子顕微鏡に関するよくある質問に対する回答です。	+
−	=== [[電子顕微鏡のTIPS]] ===	+	==== Image processing using the [[Mathematical morphology]] ====
−	電子顕微鏡を利用する際などのTIPSをまとめることにしました。	+
−	== [[ロードマップ|Eosの今後の発展（ロードマップ）について]] ==	+	=== [[EM Image Processing]] ===
−	Eosの今後の開発方針([[ロードマップ]])について述べます。	+	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.
−	== [[EosFAQ | FAQ]] ==	+	==== [[CTF Collection]] ====
−	よくある質問をまとめました。まだまだ不十分ですが、少しずつ増やしていきたいと思います。	+	EM image has received the image modulation in principle. It is the image processing to correct the image modulation.
−	== [[EosのTIPS]] ==	+	==== [[Alignment of 3D objects]] ====
−	よくある画像処理法をまとめてました。まだまだ不十分ですが、少しずつ増やしていきたいと思います。	+	It is a method for removing noise by averaging the three-dimensional image with each other.
−	== [[Eos関連ソフトウェアのTIPS]] ==	+	==== [[Alignment of a series of images]] ====
−	Eosに関連するソフトウェアの使い方をまとめています。	+	It is a method for reconstructing a three-dimensional image by combining the position of the image between the serial sections.
−	== 開発にかける思い ==	+	=== [[3D Reconstruction]] ===
−	開発当時と比べても非常に多くのソフトウェアが開発され、利用されている。その中で、継続的に開発していく意味はどこにあるのだろうか。[[開発にかける思いByYasunaga]]を少しずつ書き綴っていこう。	+	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]]====
		+	==== [[Backprojection]]====
		+
		+	==== [[SIRT]]====
		+
		+	== [[Electron Microscope]] ==
		+	We here describe electron microscopy.
		+
		+	=== [[Electron gun]]===
		+	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.
		+
		+	== [[Loadmap|The future of Eos]] ==
		+	The future of Eos ([[Loadmap]]) is shown here.
		+
		+	== FAQ and TIPS ==
		+	===  [[EosFAQ | FAQ]] ===
		+	We here plan to collenct FAQ(Frequenty asked question).
		+
		+	=== [[Eos TIPS| Eos TIPS]] ===
		+	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 ==		== Eos User Group ==
−	Eosを利用する上での情報共有の場を、仮にFacebookの上に作りました。参加されたい方は、facebook上で登録をお願いします。	+	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 [http://meta.wikimedia.org/wiki/Main_Page User's Guid]
−	== '''イメージイラストについて''' ==	+	== Tools and Sites related to Eos ==
		+	=== Programming languages ===
		+	*[[C]]
		+	*[[C++]]
		+	*[[Ruby]]
		+	*[[Tcl]]
		+	*[[Tk]]
−	現在、Eospediaのイメージイラストを募集中です。	+	=== Related workflow(PIONE) ===
−	我こそはという方はEospedia管理者まで御連絡下さい。	+	==== Petri Net ====
		+	*[[PNML]]
		+	*[[WoPeD]]
		+	==== Action description ====
		+	*[[markdown]]
		+	==== Log file ====
		+	*[[ProM]]:
		+	*[[XES]]:
−	Eospedia(WIKI)の使い方・設定に関しては、[http://meta.wikimedia.org/wiki/Main_Page ユーザーズガイド]を参照して下さい。	+	=== Documentation tools ===
		+	*[[Pandoc]]
		+	*[[html]]
		+	*[[mediawiki]]
−	== External linke ==	+	== '''External link''' ==
	* [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ Eospedia.jp]		* [http://www.yasunaga-lab.bio.kyutech.ac.jp/EosJ/ Eospedia.jp]
	* [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/ Eospedia.en]		* [http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/ Eospedia.en]
Line 249:		Line 347:
	* [http://emdatabank.org/emsoftware.html EM Software on EMDataBank]		* [http://emdatabank.org/emsoftware.html EM Software on EMDataBank]
−	== How to use mediawiki  ==	+	== '''How to use mediawiki''' ==
	* [http://www.mediawiki.org/wiki/Manual:Configuration_settings/ Configuration Settings]		* [http://www.mediawiki.org/wiki/Manual:Configuration_settings/ Configuration Settings]
	* [http://www.mediawiki.org/wiki/Manual:FAQ/ FAQ]		* [http://www.mediawiki.org/wiki/Manual:FAQ/ FAQ]
	* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce/ mediawiki-announce]		* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce/ mediawiki-announce]

---

Latest revision as of 06:26, 7 July 2017

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.

Installation

Required 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

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.

• 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 transform

Simple image processing using Eos　

Simple image processing and analysis can be performed here.

• Simple Image Processing

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.

• 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. 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.

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 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.

CTF, PSF and MTF

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

Sampling

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

Quantization

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.

Smoothing

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.

Binarization

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

Backprojection

SIRT

Electron Microscope

We here describe electron microscopy.

Electron gun

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.

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

• C
• C++
• Ruby
• Tcl
• Tk

Related workflow(PIONE)

Petri Net

• PNML
• WoPeD

Action description

• markdown

Log file

• ProM:
• XES:

Documentation tools

• Pandoc
• html
• mediawiki

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