Kinoshita at 07:25, 29 July 2014

2014-07-29T07:25:14Z

Kinoshita: /* Main option */

2014-07-18T01:58:06Z

‎Main option

Kinoshita: /* Main option */

2014-07-18T01:56:35Z

‎Main option

Kinoshita at 01:27, 18 July 2014

2014-07-18T01:27:47Z

Kinoshita: Created page with "'''mrcImageCTFCompensation''' is Eos's Command that 透過型電子顕微鏡で撮影されたmrcImage形式のファイルに対して、そのCTF([[コント..."

2014-07-18T01:21:37Z

Created page with "'''mrcImageCTFCompensation''' is Eos's Command that 透過型電子顕微鏡で撮影されたmrcImage形式のファイルに対して、そのCTF([[コント..."

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'''mrcImageCTFCompensation''' is [[Eos]]'s [[Command]] that 透過型電子顕微鏡で撮影された[[mrcImage]]形式のファイルに対して、その[[CTF]]([[コントラスト伝達関数]])を補正する.

== List of option ==
=== Main option ===
<table border="1">
<div align="left">
<tr>
<th>Option</th>
<th>Essential/Optional</th>
<th>Description</th>
<th>Default</th>
</tr>
<tr>
<td>-i</td>
<td>Essential</td>
<td>Input: [[mrcImage]](FFT)</td>
<td>stdin</td>
</tr>
<tr>
<td>-o</td>
<td>Essential</td>
<td>Output: [[mrcImage]]</td>
<td>stdout</td>
</tr>
<tr>
<td>-info</td>
<td>Optional</td>
<td>CTF information: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-info2</td>
<td>Optional</td>
<td>CTF information2: [[ASCII]]</td>
<td>NULL</td>
</tr>
<tr>
<td>-kV</td>
<td>Optional</td>
<td>[[加速電圧]][kV]</td>
<td>200</td>
</tr>
<tr>
<td>-Cs</td>
<td>Optional</td>
<td>[[球面収差係数]][mm]</td>
<td>2.1</td>
</tr>
<tr>
<td>-df</td>
<td>Optional</td>
<td>Defocus(under is +): [A]</td>
<td>27000</td>
</tr>
<tr>
<td>-white</td>
<td>Optional</td>
<td>WhiteNoise(Noise/Signal)</td>
<td>0.1</td>
</tr>
<tr>
<td>-SinWin</td>
<td>Optional</td>
<td>Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.: (SinWinRmin, SinWinRmax)</td>
<td>補正なし</td>
</tr>
<tr>
<td>-A</td>
<td>Optional</td>
<td>The ratio of amplitude contrast to phase contrast(Amplitude/Phase)</td>
<td>0.1</td>
</tr>
<tr>
<td>-Astig</td>
<td>Optional</td>
<td>With Astigmatism (difMin, dfMax, asAxis))</td>
<td>(0, 0 , 0)</td>
</tr>
<tr>
<td>-NoAstig</td>
<td>Optional</td>
<td>Without Astigmatism</td>
<td></td>
</tr>
<tr>
<td>-c</td>
<td>Optional</td>
<td>ConfigurationFile</td>
<td>NULL</td>
</tr>
<tr>
<td>-m</td>
<td>Optional</td>
<td>Mode</td>
<td>0</td>
</tr>
<tr>
<td>-h</td>
<td>Optional</td>
<td>Help</td>
<td>　</td>
</tr>
</div>
</table>
<div>If you set -NoAstig, -Astig, -Info2 are ignored.</div>
 

=== -m details ===
<table border="1">
<div align="left">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>No Correction</td>
</tr>
<tr>
<td>1</td>
<td>x ctf/|ctf| phase flipping</td>
</tr>
<tr>
<td>2</td>
<td>x ctf phase flipping and ctf-multiplying</td>
</tr>
<tr>
<td>3</td>
<td>x 1/ctf (0.1<|ctf| ) phase flipping and ctf-divided</td>
</tr>
<tr>
<td>4</td>
<td>x ctf/(SQR(ctf)+SQR(NS)) phase-flipping + Winner Filtering</td>
</tr>
<tr>
<td>5</td>
<td>x SQR(ctf) x ctf/|ctf| phase-flipping + ctf-Weighted</td>
</tr>
<tr>
<td>6</td>
<td>x 1/|ctf| (0.1<|ctf|) No phase-flipping + ctf-divided</td>
</tr>
<tr>
<td>7</td>
<td>x |ctf|/(SQR(ctf)+SQR(NS)) No phase flipping + Winner Filtering </td>
</tr>
<tr>
<td>8</td>
<td>x ctf /(SQR(ctf)+SQR(NS*exp(a*R))) phase flipping + Winner Filtering + NS-raising </td>
</tr>
<tr>
<td>9</td>
<td>x |ctf|/(SQR(ctf)+SQR(NS*exp(a*R))) No phase flipping + Winner Filtering + NS-raising </td>
</tr>
</div>
</table>
 

===-info format===
<pre>
defocus Cs kV AmplitudeContrast
</pre>
<div>By [[llExtractWithLayerSeparationFilamentInfo]](-oI)</div>
 

===-info2 format===
<div>By [[ctfDisplay]](-o) or [[Display2]]</div>
 

== Execution example ==
===[[:Media:Input-B120-CTF.fft | Input file]] image===
<table>
<tr>
<td>[[File:Input-B120-CTF.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0.000514398 (78, 51, 0) 
1684.3 (0, 0, 0) 
9.67542 
65.3969 
0.817461 
</td>
</tr>
</table>
 

===-info data===
<div>CTF information</div>
<pre>
27000.000000 2.100000 200.000000 0.100000

</pre>
 

===[[Media:Input-B120.ctfinfo|-info2 のデータ]]===
<div>CTF information2</div>
<pre>
...

ElaRShift: 0.25
flagAliasing: 1
9,NyquistFrequency: 0.2
ThonRingCanvas: 1
0,graph: .graph.graph0.graph
InElaShift: 0.0108
defocus2D0: 27000
defocus2D1: 27000

...
</pre>
 

=== Example of options only essential ===
<table>
<tr>
<td>[[File:Outdata-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-298.592 (37, 36, 0) 
46.4642 (56, 19, 0) 
-21.0538 
52.1224 
0.65153 
</td>
</tr>
</table>
 

=== Option -m===
====Case: m=1, kV=200====
=====Case: No other settings=====
<table>
<tr>
<td>[[File:Outdata-m1kV-mrcImageCTFCompensation.png]] </td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>0 (0, 0, 0) 
0 (0, 0, 0) 
0 
0 
0 
</td>
</tr>
</table>
 

=====Case: info=CTF information=====
<table>
<tr>
<td>[[File:Outdata-m1info-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-38.9125 (41, 61, 0) 
268.151 (39, 35, 0) 
21.0538 
52.1224 
0.65153 
</td>
</tr>
</table>
 

=====Case: info2=CTF information2=====
<table>
<tr>
<td>[[File:Outdata-m1info2-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-38.9125 (41, 61, 0) 
268.151 (39, 35, 0) 
21.0538 
52.1224 
0.65153 
</td>
</tr>
</table>
 

=====Case: Cs=2.1=====
<table>
<tr>
<td>[[File:Outdata-m1Cs-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-277.543 (37, 36, 0) 
67.5181 (56, 19, 0) 
-1.29646e-08 
52.1224 
0.65153 
</td>
</tr>
</table>
 

=====Case: df=27000=====
<table>
<tr>
<td>[[File:Outdata-m1df-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-59.6211 (51, 54, 0) 
244.573 (39, 35, 0) 
1.41363e-08 
52.1224 
0.65153 
</td>
</tr>
</table>
 

=====Case: A=0.1=====
<table>
<tr>
<td>[[File:Outdata-m1A-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-46.4642 (56, 19, 0) 
298.592 (37, 36, 0) 
21.0538 
52.1224 
0.65153 
</td>
</tr>
</table>
 

=====Case: Astig=(2000, 3000, 30)=====
<table>
<tr>
<td>[[File:Outdata-m1Astig-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-63.7102 (56, 19, 0) 
278.233 (37, 35, 0) 
-2.56419e-07 
52.1224 
0.65153 
</td>
</tr>
</table>
 

====Case: m=2, info=CTF information====
<table>
<tr>
<td>[[File:Outdata-m2-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-62.4959 (28, 30, 0) 
115.688 (39, 34, 0) 
2.10538 
20.8081 
0.260101 
</td>
</tr>
</table>
 

====Case: m=3, info=CTF information====
<table>
<tr>
<td>[[File:Outdata-m3-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-49.5112 (2, 15, 0) 
1120.94 (39, 39, 0) 
210.538 
256.745 
3.20931 
</td>
</tr>
</table>
 

====Case: m=4, info=CTF information====
=====Case: No other settings=====
<table>
<tr>
<td>[[File:Outdata-m4-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-76.6069 (1, 16, 0) 
835.557 (40, 39, 0) 
105.269 
192.376 
2.4047 
</td>
</tr>
</table>
 

=====Case: white=0.5=====
<table>
<tr>
<td>[[File:Outdata-m4white-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-59.6252 (50, 54, 0) 
195.105 (39, 35, 0) 
8.0976 
38.5767 
0.482208 
</td>
</tr>
</table>
 

====Case: m=5, info=CTF information====
<table>
<tr>
<td>[[File:Outdata-m5-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-63.7521 (29, 30, 0) 
81.6286 (39, 34, 0) 
0.210538 
16.0662 
0.200828 
</td>
</tr>
</table>
 

====Case: m=6, info=CTF information====
<table>
<tr>
<td>[[File:Outdata-m6-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-1338.09 (37, 36, 0) 
212.611 (2, 70, 0) 
-210.538 
272.238 
3.40297 
</td>
</tr>
</table>
 

====Case: m=7, info=CTF information====
=====Case: No other settings=====
<table>
<tr>
<td>[[File:Outdata-m7-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-885.311 (37, 36, 0) 
43.1237 (2, 0, 0) 
-105.269 
192.376 
2.4047 
</td>
</tr>
</table>
 

=====Case: white=0.5=====
<table>
<tr>
<td>[[File:Outdata-m7white-mrcImageCTFCompensation.png]]</td>
<td>Min 
Max 
Mean 
SD 
SE 
</td>
<td>-221.279 (37, 36, 0) 
60.2085 (29, 27, 0) 
-8.0976 
38.5767 
0.482208 
</td>
</tr>
</table>

← Older revision		Revision as of 07:25, 29 July 2014
Line 1:		Line 1:
−	'''mrcImageCTFCompensation''' is [[Eos]]'s [[Command]] that corrects [[CTF]] ([[Contrast ~~transfer function~~]]) for [[mrcImage]] files taken by a transmission electron microscope.	+	'''mrcImageCTFCompensation''' is [[Eos]]'s [[Command]] that corrects [[CTF]] ([[Contrast Transfer Function]]) for [[mrcImage]] files taken by a transmission electron microscope.

	== List of option ==		== List of option ==

← Older revision		Revision as of 01:27, 18 July 2014
Line 1:		Line 1:
−	'''mrcImageCTFCompensation''' is [[Eos]]'s [[Command]] that ~~透過型電子顕微鏡で撮影された~~[[~~mrcImage~~]]~~形式のファイルに対して、その~~[[~~CTF~~]]([[~~コントラスト伝達関数~~]]~~)を補正する~~.	+	'''mrcImageCTFCompensation''' is [[Eos]]'s [[Command]] that corrects [[CTF]] ([[Contrast transfer function]]) for [[mrcImage]] files taken by a transmission electron microscope.

	== List of option ==		== List of option ==

@@ Line 44: / Line 44: @@
 				<td>-Cs</td>
 				<td>Optional</td>
-				<td>[[球面収差係数]][mm]</td>
+				<td>[[Spherical aberration coefficient]][mm]</td>
 				<td>2.1</td>
 			</tr>

@@ Line 38: / Line 38: @@
 				<td>-kV</td>
 				<td>Optional</td>
-				<td>[[加速電圧]][kV]</td>
+				<td>[[Acceleration voltage]][kV]</td>
 				<td>200</td>
 			</tr>

mrcImageCTFCompensation - Revision history

Kinoshita at 07:25, 29 July 2014

Kinoshita: /* Main option */

Kinoshita: /* Main option */

Kinoshita at 01:27, 18 July 2014

Kinoshita: Created page with "'''mrcImageCTFCompensation''' is Eos's Command that 透過型電子顕微鏡で撮影されたmrcImage形式のファイルに対して、そのCTF([[コント..."