Functional Order of Commands

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We here sort commands in functional orders, but not yet. We are very sorry for being too late for you.

Contents

Overviers and template

We classify Eos commands into functional groups. templateCommandWiki: template to write down a help of commands.

Integration tools/platform

Image View and Image Analysis

  • Display2: To display a 2D image or a section of a 3D image, process them, and pick ROIs(region of interest) from an image.

cf.Particle Picking by Display2

  • Display3: To display a 3D image
  • smolet: To display a series of tilt images for electron tomography.
  • ctfDisplay: To display a Fourier transform for CTF correlation
  • imagesClustering: To display a dendrogram for image clustering.

Platform in Eos

  • Visualmake: Easy and automatics GUI generator for Makefile
  • Eos: Eos on Tcl/Tk, CUI
  • PIONE: PIONE(Process-rule for Input/Output Negotiation Enviromenment) is a rule-based workflow engine.

Easy and Simple Viewers in Eos

A series of molvie (2D-3D seamless viewers)

Developmental environment on Eos

to create a new command or object

to create a new one automatically using 'make'

A series of commands for CTF and its correction　

Tools for CTF functions

Tools for CTF/defocusing value detemination

Tools for CTF correction

a platform

CTF Function

CTF Determination

CTF Correction

etc.

Tools for image clustering

3D reconstruction　

General tools for 3D reconstruction

  • mrc2Dto3D：a tool for a 3D reconstruction from a set of 2D images.
  • mrc3Dto2D：a tool for a set of 2D projection images from a 3D object.
  • mrc2Dto3DforVariation：a tool for the variance of a 3D reconstruction from a set of 2D images.
  • mrcRadon2Dto3D：a tool for a 3D Radon space from a set of 2D Radon images.

Back-projection of 2D images

Tools for tomography

Tools for single particle analysis

Tools for analysis of images in Radon space

Tools for a transform in Radon Space


Tools for common line search

Sinogram analysis using feature

3D reconstruction using feature

3D reconstruction using helical symmetry

Space transformation

Tools for (Layer Line Extraction) llExtract

Tools for G(R, THETA, Z) space

Tools for g(r, theta, Z) space

Image analysis using helical symmetry

Tools for super-resolutions

Tools to check spatial resolutions

Tools for mrcImage-formated images

Tools for mrcImage-format

Tools to create models

A basic shape model creation

Addition of noise

Crystallization

Tilted images

Infomation of images

Statistics of images

  • mrcImageFeatureExtraction：画像の特徴量（現時点で３０通り）の抽出
    • ヒストグラムの平均、分散、歪度、尖度、コントラスト、エネルギー、エントロピー
    • Co-occurenceに関する情報
    • difference statisticsに関する情報
    • runlengthに関する情報

Image alignment using object-shape

  • mrcImageShapePCA：３Ｄ画像からその構造の形を楕円体として取り扱うための主成分分析
  • mrcImageShapePCAFit：３Ｄ画像からその構造の形を楕円体として取り扱い、主軸同士を合わせるための処理

Image-fomart transform

Analysis of multi-images

  • mrcImageMontageCreate：複数枚の画像を一枚の画像として出力する（平均値等を用いて画像のコントラストを合わす）

Pre-treatment of images

Removal of abnormal values

Windowoing

Padding

Standalization of density

Unitary operator for a image

  • ２乗和
    • mrcImageSquare:各ピクセル値の２乗、ルートの画像に変換する。

Binary operator between images

  • 和算

Mathematical morphology

  • オープニング（白いひげが消えるが、孔は保たれる）
  • クロージング（黒い孔（谷）が埋まるが、丘は高くならない）

Extraction of ROI(Region of Interest)

  • mrcImageROI：２次元画像からの単一のROI画像の切り出し
  • mrcImageROIs：２次元画像からの複数のROI画像の切り出し
  • mrcImageUnbentROI：２次元画像からのスプライン曲線に則った切り出し

Image overlay and split

Automatic particle extraction

Density transfomr

Resampling

Masking

  • mrcImageMasking：定型の円や長方形で画像をマスクする（３Ｄに対応）
  • mrcImageMaskingByImage:画像（２値化もしくはグレー）を用いて画像をマスクする。
  • mrcImageFilterCreate:指定した座標値の所を指定した値とした画像を作り出す。

Rotation and Shift of image

Binary Image analysis　

Binarization

Connectivity

Labeling and Area calculation

Coordinate tranform

Fourier Transform

  • mrcImageFFT：現在、通常使われているフーリエ変換及び逆変換
  • fft2d：過去のフーリエ変換及び逆変換
  • cufft：CUDAでのテスト用フーリエ変換

Filter for spatial frequency

Smoothing

  • mrcImageSmoothing：非線形の平滑化
    • median filter（中央値フィルタ）
    • mean filter(平均値フィルタ)
    • SurfaceFit filter（最小自乗法により２次曲面に近似）
    • Lee-sigma filter（シグマフィルタ）
  • mrcImageLowPassFilter:ローパスフィルタ（周波数空間でのフィルタ）
    • Step filter(Ideal Filter)（矩形窓（方形窓）関数によるフィルタ）
    • Cos filter（テューキー窓によるフィルタ）
    • Exponetial filter（指数窓によるフィルタ）
    • Gaussian filter（ガウス窓によるフィルタ）
    • Lorentzian filter（ローレンチアンによるフィルタ）
  • mrcImageBilateralFilter:バイラテラルフィルタ（像強度による重み付き平滑化フィルタ）
  • mrcImageNLMeansFilter:NLミーンズ法によるローパスフィルタ
  • mrcImageNoiseReductionByRelaxation:緩和法によるノイズ除去

Edge extraction

Similarity between images

Image analysis using symmetry


Tools for mrcFFT（Fourier Space) Information　

Printing tools

mrcRef-related analysis

Tools using PDB-format for image analysis

Energy-loss images　

Not Classified


Tools for PDB information

Atomic coordinate information for PDB files

Density map creation from atomic coordinates of PDB


Other format from PDB

Atomic coordinates creation using symmetry

Rotation and Move of atomic coordinates in PDB

Fitting procedure between atomic coordinates in PDB file and density map

Displaying of PDB

Additional data for PDB

ETC

filters for image-format transformation

From other format to mrc-image format

From MRC-image format to other format　

Related to pgFormat

Tools for postscript

Related to DCD format

etc.


Various analysis tools

Tools for atomic coordinate modeling using initial coordinates and density

Reference:

  • Noda et al., J. Plasma, Physics (2006)
  • Murakami et al., Cell (2010)

Tools for FRET analysis

References:

  • Suzuki et al., Nature (1998)
  • Yasunaga e al., J.Struct.Biol.(2000)

ETC

Tools for molecular information handling

Tools for matrix3D (4x4 matrix for 3D transfomation)

Generation of random number

tools for largeIP

Tools for points

Control for TEM

System test tools

ETC

Not yet

CheckCommonLineData CheckOfOrientation CheckOrientationByDegree


LCalculationForOrientationSearch

ProjectionDirectionMapCreate

TestForLcalculationOfOrientationSearchBySimultaneousMinimization


angleMatchTest_k anglediffcalc anglediffchk

calcCommonLine

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