Difference between revisions of "ctfDisplay"

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== Execution example ==
 
== Execution example ==
 
　Here, Here, determine CTF Parameters by using provided data and [[ctfDisplay]].
 
　Here, Here, determine CTF Parameters by using provided data and [[ctfDisplay]].
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First, execute most simple way. Beforehand, get [[:Media:example.fft]] by Fourier Transformation of [[:Media:example.mrc]] by [[mrcImageFFT]].
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First, execute most simple way. Beforehand, get [[Media:example.fft]] by Fourier Transformation of [[Media:example.mrc]] by [[mrcImageFFT]].
  
 
Then, determinate Parameters(e.g. Defocus) by using [[ctfDisplay]].
 
Then, determinate Parameters(e.g. Defocus) by using [[ctfDisplay]].
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  $ ctfDisplay -i example.fft -o example.ctfinfo
 
  $ ctfDisplay -i example.fft -o example.ctfinfo
  
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It can execute by the above command. .ctfinfoのファイルは、指定されない場合も自動的に設定され、存在している場合には、そのデータを読み込んできます。その結果、下記のようなウィンドウが開きます。
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It can execute by the above command. If .ctfinfo file is exist, its data is read. Otherwise, it is set automatically. And, the following window opens.
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[[ファイル:ctfDisplay-startup.png|center|512px]]
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[[File:ctfDisplay-startup.png|center|512px]]
  
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この中で、左側の画面がフーリエ変換したスペクトラムを、まん中が、そのスペクトラムを角度方向に平均したもの、右がCTFのための各種パラメータになっています。
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The left side of window displays the spectrum of Fourier Transformation, the middle side displays the spectrum's average by angle, and the right side shows each parameter for CTF.
  
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下記の手順で、ＣＴＦ関数を見積もります。
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Calculate CTF Function by the following method.
  
  
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１．スペクトラムがでるようにImin/Imaxを調整します。Logのボタンをおしたほうが見つかりやすいことが多いです。よくわからなかったら、Imin=0.00001, Imax=100000　とし、Logボタンを押せば、どこかに青色のスペクトラムが現れると思います。あとは、そのスペクトラムの範囲をよく見て設定して下さい。最初から分かっているときには、起動時に
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1. Align Imin/Imax so that the spectrum can be seen. Pushing Log  button may be easy to see. If you can't see it, set Imin=0.00001, Imax=100000 and push Log button. Then, there is blue spectrum on somewhere. After that, set range of this spectrum with looking carefully. If you know the range beforehand, at executing
  
 
  $ ctfDisplay -i example.fft -o example.ctfinfo -Imin 0.01 -Imax 100 -Log
 
  $ ctfDisplay -i example.fft -o example.ctfinfo -Imin 0.01 -Imax 100 -Log
  
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とし、最大値と最小値を設定すれば最初から直視することができます。
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By setting Max Value and Min Value, you can already see it.
  
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２．同様に自分が見たい範囲で、Rmax[/A]を設定して下さい。Rmax=0.1が1nm, Rmax=0.5が2A, Rmax=1が1Aを示しています。Rminはあまり変更する必要はありません。
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2. As well, set Rmax[/A] range as you want to see. Rmax=0.1 means 1nm, Rmax=0.5 means 2A, and Rmax=1 means 1A. Rmin doesn't usually have to change.
  
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３．次に、ノイズのレベルを合わせます。この操作は、ＣＴＦ補正そのものには通常は関係しませんが、ＣＴＦを決定する際に便利です。合わせるためのパラメータは、Inoise、MTF0もしくは、MTF1です。CCDやフィルムなどメディアに応じて、MTFの形がe指数関数型かローレンツ型を選択することができます。MTF0が指数関数型のパラメータ、MTF1がローレンツ型のパラメータです。
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3. Next, align the noise level. This operation doesn't relate to CTF Correction normally, but it is useful determining CTF. For aligning it, set the parameters Inoise, MTF0 or MTF1. Depending to the media as CCD or Film, you can select either Exponential or Lorentzian about the shape of MTF. MTF0 is Exponential parameter, and MTF1 is Lorentzian parameter.
  
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４．シグナルのレベルを合わせます。まずは、Inoiseと同じ値をIsignalに設定して下さい。
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4. Align the signal level. First, Isignal set the same value as Inoise.
  
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５．ＣＴＦのパラメータを設定します。画面右下にあります。
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5. Set CTF parameter. Look at the right bottom of window.
  
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　５−１：kV: [[加速電圧]][kV]の設定
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　5-1:kV: Setting [[Acceleration voltage]][kV]
  
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　５−２： Cs/Cc: [[球面収差係数]] [[Cs]][mm], 色収差係数 [[Cc]][mm]の設定
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　5-2: Cs/Cc: Setting [[Spherical aberration coefficient]] [[Cs]][mm], Chromatic aberration coefficient [[Cc]][mm]
  
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　５−３：Ai: [[照射半角]]であるAi[mrad]の設定(LaB6で0.15-0.45程度、サーマルフィールドでは0.03-0.05程度、コールドフィールドでは0.02-0.04程度が目安です。条件によって異なります。）
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　5-3: Ai: Setting [[Illumination Aperture]] Ai[mrad] (e.g. LaB6: about 0.15-0.45(in Normal Field), 0.03-0.05(in Thermal Field), 0.02-0.04(in Cold Field): The value is different according to situation.)
  
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　　　　　この値に関しては、最終的にフィッティングするとシグナルがよく説明出来ます。撮影条件によって同じ電子銃でも変わります。撮影条件を考える上で重要なパラメータの一つです。
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　　　　　Speaking about this value, Fitting can explain the signal finally. Even if you use same Electron gun, the value might be different according to situations. It is one of important parameter for considering the projection environment.
  
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　５−４：nDivision: 分割数の設定：通常は変更する必要はありません。どうしてもＳＮが悪いときにこの値を下げてみて下さい。
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　5-4: nDivision: Setting number of division: It usually needs not to change. If SN is not good, try to lower this value.
  
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６．デフォーカスを決定していきます。
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6. Determine Defocus.
  
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　６−１　トーンリングが楕円になっている場合には、楕円の長軸と短軸にそれぞれ０軸、１軸のそれぞれが合うように、AxisFor0の角度を設定して下さい。長軸と短軸はどちらが０軸でも問題ありません。うまく軸があった時が、一番シグナル（青い線）の凹凸がはっきりします。
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　6-1: If Thon Ring is the ellipsoid, set AxisFor0 Angle as the longer and shorter axis are 0-axis or 1-axis. Both axis is fine. When these axis fit better, you can see the Irregularities of signal(blue line) more clearly.
  
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　６−２　窪み（トーンリング）の所に、ＣＴＦ関数（赤い線）の谷がくるようにデフォーカスの値をdefocus0/defocus1のそれぞれを変更して下さい。縦線がトーンリングの位置を表します。
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　6-2: Change each value of defocus0/defocus1 as fitting the dent(Thon Ring) to valley of CTF(red line). Vertical line means Thon Ring.
  
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　６−３　Isignal/Ai/defocusをうまく合わせると第一トーンリングの所の形がよく説明できます。
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　6-3: When Isignal/Ai/defocus fit better, it can explain the shape on 1st Thon Ring.
  
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全体がうまく設定できると、下記のようになります。
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The following is the example of good setting on the whole.
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[[ファイル:ctfDisplay-example.png|center|840px]]
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[[File:ctfDisplay-example.png|center|840px]]
  
  
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７．Saveボタンを押して保存します。
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7. Save with pushing Save button.
  
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８．終了は、ウィンドウを閉じる、qのキーを押す、saveAndExit, Exitのボタンを押すのいずれかで実行できます。
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8. Exit with closing the window, or pushing q key, or pushing saveAndExit button or Exit button.

Latest revision as of 08:06, 25 August 2014

ctfDisplay is one of Integration Tools(Integration Commands) for setting CTF Parameters (e.g. Defocus). There is the command that determines CTF Parameters automatically. But, In the case of low contrast or low SN-Ratio(e.g. using cryo-EM data), or checking automatically determined data as defocus, use it.

List of option

Main option

Option Essential/Optional Description Default
-i Optional Input: mrcImage(FFT) NULL
-o Optional Input and Output: ASCII(CTF Information) stdout
-Rmax Optional Rmax: [A-1] 0.2
-Imax Optional Intensity max 0.2
-Imin Optional Intensity min 0.2
-AutoRange Optional
-Log Optional Log of Intensity
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　
-o 's Input and Output file can be used by mrcImageCTFCompensation.

-m details

Value Description
0

Execution example

　Here, Here, determine CTF Parameters by using provided data and ctfDisplay. First, execute most simple way. Beforehand, get Media:example.fft by Fourier Transformation of Media:example.mrc by mrcImageFFT.

Then, determinate Parameters(e.g. Defocus) by using ctfDisplay. 

$ mrcImageFFT -i example.mrc -o example.fft
$ ctfDisplay -i example.fft -o example.ctfinfo

Determined CTF Parameters are stored in example.ctfinfo file. Next, perform CTF Correction by using this file.

The following shows how to use the ctfDisplay. Download the data at here. 

$ ctfDisplay -i example.fft -o example.ctfinfo

It can execute by the above command. If .ctfinfo file is exist, its data is read. Otherwise, it is set automatically. And, the following window opens.

ctfDisplay-startup.png

The left side of window displays the spectrum of Fourier Transformation, the middle side displays the spectrum's average by angle, and the right side shows each parameter for CTF.

Calculate CTF Function by the following method.


1. Align Imin/Imax so that the spectrum can be seen. Pushing Log button may be easy to see. If you can't see it, set Imin=0.00001, Imax=100000 and push Log button. Then, there is blue spectrum on somewhere. After that, set range of this spectrum with looking carefully. If you know the range beforehand, at executing 

$ ctfDisplay -i example.fft -o example.ctfinfo -Imin 0.01 -Imax 100 -Log

By setting Max Value and Min Value, you can already see it.

2. As well, set Rmax[/A] range as you want to see. Rmax=0.1 means 1nm, Rmax=0.5 means 2A, and Rmax=1 means 1A. Rmin doesn't usually have to change.

3. Next, align the noise level. This operation doesn't relate to CTF Correction normally, but it is useful determining CTF. For aligning it, set the parameters Inoise, MTF0 or MTF1. Depending to the media as CCD or Film, you can select either Exponential or Lorentzian about the shape of MTF. MTF0 is Exponential parameter, and MTF1 is Lorentzian parameter.

4. Align the signal level. First, Isignal set the same value as Inoise.

5. Set CTF parameter. Look at the right bottom of window.

　5-1:kV: Setting Acceleration voltage[kV]

　5-2: Cs/Cc: Setting Spherical aberration coefficient Cs[mm], Chromatic aberration coefficient Cc[mm]

　5-3: Ai: Setting Illumination Aperture Ai[mrad] (e.g. LaB6: about 0.15-0.45(in Normal Field), 0.03-0.05(in Thermal Field), 0.02-0.04(in Cold Field): The value is different according to situation.)

　　　　　Speaking about this value, Fitting can explain the signal finally. Even if you use same Electron gun, the value might be different according to situations. It is one of important parameter for considering the projection environment.

　5-4: nDivision: Setting number of division: It usually needs not to change. If SN is not good, try to lower this value.

6. Determine Defocus.

　6-1: If Thon Ring is the ellipsoid, set AxisFor0 Angle as the longer and shorter axis are 0-axis or 1-axis. Both axis is fine. When these axis fit better, you can see the Irregularities of signal(blue line) more clearly.

　6-2: Change each value of defocus0/defocus1 as fitting the dent(Thon Ring) to valley of CTF(red line). Vertical line means Thon Ring.

　6-3: When Isignal/Ai/defocus fit better, it can explain the shape on 1st Thon Ring.

The following is the example of good setting on the whole.

ctfDisplay-example.png


7. Save with pushing Save button.

8. Exit with closing the window, or pushing q key, or pushing saveAndExit button or Exit button.

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