Kinoshita at 07:29, 1 October 2014

2014-10-01T07:29:49Z

Kinoshita at 07:29, 1 October 2014

2014-10-01T07:29:02Z

Kinoshita: /* Main option */

2014-10-01T06:52:46Z

‎Main option

Kinoshita: /* List of option */

2014-10-01T06:45:29Z

‎List of option

Kinoshita: /* Main option */

2014-07-18T01:57:25Z

‎Main option

Kinoshita: /* Main option */

2014-07-18T01:56:17Z

‎Main option

Kinoshita: Created page with "'''mrcImageCTFDetermination''' is Eos's Command for the estimation of the CTF。 == List of option == === Main option ===

Optio..."
2014-07-18T01:54:31Z

Created page with "'''mrcImageCTFDetermination''' is Eos's Command for the estimation of the CTF。 == List of option == === Main option === <table border="1"> <tr> <th>Optio..."

New page
'''mrcImageCTFDetermination''' is [[Eos]]'s [[Command]] for the estimation of the CTF。

== List of option ==
=== Main option ===
<table border="1">
<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]](M=0, 1: FFT, M=2: 2D)</td>
<td>NULL</td>
</tr>
<tr>
<td>-r</td>
<td>Essential</td>
<td>Reference: [[mrcImage]](M=0: FFT, M=1: llData, M=2: 2D)</td>
<td>NULL</td>
</tr>
<tr>
<td>-o</td>
<td>Optional</td>
<td>Output: Optimum: [[ASCII]](For M=0)<br>
defocus and amplitude-contrast at minimum point</td>
<td>stdout</td>
</tr>
<tr>
<td>-oP</td>
<td>Optional</td>
<td>Output: Distribution: [[mrcImage]](For M=0)</td>
<td>NULL</td>
</tr>
<tr>
<td>-oC</td>
<td>Optional</td>
<td>Output: [[CTF information]]: [[ASCII]](using -mC)</td>
<td>NULL</td>
</tr>
<tr>
<td>-oF</td>
<td>Optional</td>
<td>Output: Result FFT: [[mrcImage]](For M=2)</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: [mm]</td>
<td>2.1</td>
</tr>
<tr>
<td>-Ain</td>
<td>Optional</td>
<td>IlluminationAperture[mrad]</td>
<td>0.02</td>
</tr>
<tr>
<td>-W</td>
<td>Optional</td>
<td>WhiteNoise(Noise/Signal)</td>
<td>1.0</td>
</tr>
<tr>
<td>-df</td>
<td>Optional</td>
<td>Defocus: [A]: (mindf, maxdf, deldf)</td>
<td>(0.0, 200000, 1000)</td>
</tr>
<tr>
<td>-AoverP</td>
<td>Optional</td>
<td>AoverP[A] for in(minAoverP, maxAoverP, delAoverP)</td>
<td>(0.0, 1.0, 0.01)</td>
</tr>
<tr>
<td>-Rmin</td>
<td>Optional</td>
<td>Min spatial frequency[/A]</td>
<td>0.0</td>
</tr>
<tr>
<td>-Rmax</td>
<td>Optional</td>
<td>Max spatial frequency[/A]</td>
<td>0.1</td>
</tr>
<tr>
<td>-mF</td>
<td>Optional</td>
<td>:Filter Type</td>
<td>1</td>
</tr>
<tr>
<td>-mW</td>
<td>Optional</td>
<td>Wight Type</td>
<td>0</td>
</tr>
<tr>
<td>-mS</td>
<td>Optional</td>
<td>Sum Type</td>
<td>0</td>
</tr>
<tr>
<td>-mC</td>
<td>Optional</td>
<td>CTF Information Type</td>
<td>0</td>
</tr>
<tr>
<td>-M</td>
<td>Optional</td>
<td>ref Type</td>
<td>0</td>
</tr>
<tr>
<td>-PixelSize</td>
<td>Optional</td>
<td>Pixel size [A] (For M=1)</td>
<td>5</td>
</tr>
<tr>
<td>-Width</td>
<td>Optional</td>
<td>Pad Width [pixel] (For M=1)</td>
<td>120</td>
</tr>
<tr>
<td>-truePitch</td>
<td>Optional</td>
<td>True Pitch [A] (For M=1)</td>
<td>700</td>
</tr>
<tr>
<td>-dfRef</td>
<td>Optional</td>
<td>dfRef for ref(firstDf, withinDf) (For M=2)</td>
<td>(70000, 1000)</td>
</tr>
<tr>
<td>-AoverPRef</td>
<td>Optional</td>
<td>A over P Ref for ref(firstAoverP, withinAoverP) (For M=1, 2)</td>
<td>(0.05, 0.01)</td>
</tr>
<tr>
<td>-MaxIter</td>
<td>Optional</td>
<td>MaxIteration for ref(For M=2)</td>
<td>10</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>
</table>
<br>

===-mF details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>No CTF compensation</td>
</tr>
<tr>
<td>1</td>
<td>Phase only: W = CTF/|CTF|</td>
</tr>
<tr>
<td>2</td>
<td>Multiply : W = CTF</td>
</tr>
<tr>
<td>3</td>
<td>Multiply : W = 1/CTF</td>
</tr>
<tr>
<td>4</td>
<td>Wiener filter (constant noise): W = CTF/(|CTF|^2+N^2)</td>
</tr>
<tr>
<td>5</td>
<td>Multiply : W = CTF^2</td>
</tr>
</table>
<br>

===-mW details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Weight = 1</td>
</tr>
<tr>
<td>1</td>
<td>Weight = (|in| + |ref|)/2</td>
</tr>
</table>
<br>

===-mS details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>Sigma[Phase(i)]</td>
</tr>
<tr>
<td>1</td>
<td>Sigma[Phase(i)*Weight(i)] / Sigma[Weight(i)]</td>
</tr>
</table>
<br>

===-mC details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>[[llExtractCtfinfFileCreate]](m=0)'s format</td>
</tr>
<tr>
<td>1</td>
<td>[[llExtractCtfinfFileCreate]](m=1)'s format</td>
</tr>
</table>
<br>

===-M details===
<table border="1">
<tr>
<th>Value</th>
<th>Description</th>
</tr>
<tr>
<td>0</td>
<td>CTF compensated single image</td>
</tr>
<tr>
<td>1</td>
<td>Three-dimentional reconstruction images that were made by nea and far Bessel separation.<br>
CTF compensatation were done between min defocus to max defocus.<br>
This mode is for myosin filaments.<br>
(Options) -PixelSize, -Width, -truePitch, -dfRef, -AoverPRef, -MaxIter<br>
-i, -r: It does not correspond to the file name too long.<br></td>
</tr>
<tr>
<td>2</td>
<td>Result FFT<br>
(Options) -oF, -dfRef, -AoverPRef </td>
</tr>
</table>
<br>

== Execution example ==
=== Input file's image ===
[[Media:Input-B120-CTF.fft|M=0 file]](default)
<table>
<tr>
<td>[[File:Input-B120-CTF.png]]<br>
<td><p align="left">Size<br>
モード<br>
Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">( 80, 80, 1)<br>
mrcComplexFloatFT <br>
0.000514398 (78, 51, 0)<br>
1684.3 (0, 0, 0)<br>
9.67542<br>
65.3969<br>
0.817461<br></p>
</td>
</tr>
</table>
<br>

<div>[[Media:Input-B120-CTF.mrc|M=2 file]]</div>
<table>
<tr>
<td>[[File:Input-mrcImageCTFObservation.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">-298.592 (37, 36, 0)<br>
46.4642 (56, 19, 0)<br>
-21.0538<br>
52.1224<br>
0.65153<br></p>
</td>
</tr>
</table>
<br>

===Reference file's image===
[[Media:Input-B120.fft|M=0 file]](default)
<table>
<tr>
<td>[[File:Input-B120-FFT.png]]</td>
<td><p align="left">Size<br>
Mode<br>
Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">( 80, 80, 1)<br>
mrcComplexFloatFT <br>
0.00776821 (75, 37, 0)<br>
1684.3 (0, 0, 0)<br>
9.41977<br>
61.1799<br>
0.764749<br></p>
</td>
</tr>
</table>
<br>

<div>[[Media:Input-B120.mrc|M=2 file]]</div>
<table>
<tr>
<td>[[File:Input-B120.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0 (0, 0, 0)<br>
255 (49, 32, 0)<br>
21.0538<br>
47.6709<br>
0.595886<br></p>
</td>
</tr>
</table>
<br>

=== Example of options only essential ===
<div>-oP's image(z=0)</div>
<table>
<tr>
<td>[[File:Outdata-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.0193939 (18, 72, 0)<br>
2.0847 (13, 0, 0)<br>
1.52075<br>
0.209894<br>
0.00147313<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(18000.000000 0.720000): 0.019394
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.042155 -1 0
0.042155 0 0
</pre>
<br>

=== Option -df===
====Case: df=(0, 27000, 200)====
<div>-oP 's image(z=0)</div>
<table>
<tr>
<td>[[File:Outdata-df-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.0193939 (90, 72, 0)<br>
2.11379 (68, 0, 0)<br>
1.34909<br>
0.459847<br>
0.00392359<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.830000): 0.019394
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041808 -1 0
0.041808 0 0
</pre>
<br>

<div>In the following, Setting atdf=(0, 27000, 200)で実行</div>
=== Option -kV===
====Case: kV=100====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-kV-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.0193939 (61, 75, 0)<br>
2.09439 (46, 0, 0)<br>
1.39997<br>
0.391015<br>
0.00333628<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(12200.000000 0.750000): 0.019394
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.042014 -1 0
0.042014 0 0
</pre>
<br>

=== Option -Cs===
====Case: Cs=1.7====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-Cs-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.0193939 (89, 82, 0)<br>
2.13318 (68, 1, 0)<br>
1.34903<br>
0.459735<br>
0.00392263<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.820000): 0.019394
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041856 -1 0
0.041856 0 0
</pre>
<br>

=== Option -Ain===
====Case: Ain=0.1====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-Ain-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.0193939 (90, 72, 0)<br>
2.11379 (68, 0, 0)<br>
1.34909<br>
0.459847<br>
0.00392359<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.830000): 0.019394
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041808 -1 0
0.041808 0 0
</pre>
<br>

=== Option -AoverP===
====Case: AoverP=(0.2, 0.8, 0.02)====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-AoverP-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.0193939 (90, 26, 0)<br>
2.05561 (66, 0, 0)<br>
1.34786<br>
0.460559<br>
0.00709308<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(18000.000000 0.720000): 0.019394
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.042155 -1 0
0.042155 0 0
</pre>
<br>

=== Option -Rmin, -Rmax===
====Case: Rmin=0.02, Rmax=0.08====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-RminRmax-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">6.98324e-07 (89, 96, 0)<br>
2.35212 (50, 0, 0)<br>
1.26243<br>
0.571554<br>
0.00487671<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.959999): 0.000001
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041186 -1 0
0.041186 0 0
</pre>
<br>

=== Option -mF===
====Case: mF=0====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-M0-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">1.71139 (0, 0, 0)<br>
1.71139 (0, 0, 0)<br>
1.71139<br>
9.28666e-07<br>
7.92373e-09<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(0.000000 0.000000): 1.711393
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
-1.000000 -1 0
-1.000000 0 0
</pre>
<br>

====Case: mF=3====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-mF3-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">1.43906e-06 (89, 96, 0)<br>
2.16712 (66, 0, 0)<br>
1.35241<br>
0.46216<br>
0.00394332<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.959999): 0.000001
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041186 -1 0
0.041186 0 0
</pre>
<br>

=== Option -mC===
====mC=1====
<div>-oC 's data</div>
<pre>
17800.000000 2.100000 200.000000 0.830000
</pre>
<br>

=== Option -mW, -mS===
====Case: mW=1, mS=1====
=====Case: No other settings=====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-mWmS-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.00342354 (89, 96, 0)<br>
2.48255 (0, 0, 0)<br>
0.538199<br>
0.224044<br>
0.00191162<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.959999): 0.003424
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041186 -1 0
0.041186 0 0
</pre>
<br>

=====Case: mF=2=====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-mF2-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.00311023 (89, 100, 0)<br>
2.42005 (0, 0, 0)<br>
0.567162<br>
0.258248<br>
0.00220347<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.999999): 0.003110
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041009 -1 0
0.041009 0 0
</pre>
<br>

=====Case: mF=4=====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-mF4-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.00311023 (89, 100, 0)<br>
2.42005 (0, 0, 0)<br>
0.567162<br>
0.258248<br>
0.00220347<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.999999): 0.003110
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041009 -1 0
0.041009 0 0
</pre>
<br>

=====Case: mF=5=====
<div>-oP 's image</div>
<table>
<tr>
<td>[[File:Outdata-mF5-mrcImageCTFDetermination.png]]</td>
<td><p align="left">Min<br>
Max<br>
Mean<br>
SD<br>
SE<br></p>
</td>
<td><p align="left">0.00279326 (89, 100, 0)<br>
2.42334 (0, 0, 0)<br>
0.586665<br>
0.276375<br>
0.00235814<br></p>
</td>
</tr>
</table>

<div>-o 's data</div>
<pre>
(17800.000000 0.999999): 0.002793
</pre>

<div>-oC 's data</div>
<pre>
0.000000 -1 0
0.041009 -1 0
0.041009 0 0
</pre>
<br>

=== Option -M===
====Case: M=2====
=====Case: No other settings=====

← Older revision		Revision as of 07:29, 1 October 2014
Line 1:		Line 1:
−	'''mrcImageCTFDetermination''' is [[Eos]]'s [[Command]] for the estimation of the [[CTF]]. It outputs average phase difference with reference image or determined [[CTF Information]]. These data can be used as set data of [[ctfDisplay]].	+	'''mrcImageCTFDetermination''' is [[Eos]]'s [[Command]] for the estimation of the [[CTF]]. It outputs average phase difference with reference image or determined [[CTF Information]]. These data can be used as set data(-o) of [[ctfDisplay]].

← Older revision		Revision as of 07:29, 1 October 2014
Line 1:		Line 1:
−	'''mrcImageCTFDetermination''' is [[Eos]]'s [[Command]] for the estimation of the ~~CTF。~~	+	'''mrcImageCTFDetermination''' is [[Eos]]'s [[Command]] for the estimation of the [[CTF]]. It outputs average phase difference with reference image or determined [[CTF Information]]. These data can be used as set data of [[ctfDisplay]].

@@ Line 27: / Line 27: @@
 				<td>Optional</td>
 				<td>Output: Optimum: [[ASCII]](For M=0)<br>
-					defocus and amplitude-contrast at minimum point</td>
+					(defocus amplitude-contrast): minimum point</td>
 				<td>stdout</td>
 			</tr>

@@ Line 33: / Line 33: @@
 				<td>-oP</td>
 				<td>Optional</td>
-				<td>Output: Distribution: [[mrcImage]](For M=0)</td>
+				<td>Output: Distribution((-df) x (-AoverP)): [[mrcImage]](For M=0)</td>
 				<td>NULL</td>
 			</tr>

@@ Line 57: / Line 57: @@
 				<td>-Cs</td>
 				<td>Optional</td>
-				<td>球面収差: [mm]</td>
+				<td>[[Spherical aberration coefficient]]: [mm]</td>
 				<td>2.1</td>
 			</tr>

@@ Line 51: / Line 51: @@
 				<td>-kV</td>
 				<td>Optional</td>
-				<td>加速電圧: [kV]</td>
+				<td>[[Acceleration voltage]]: [kV]</td>
 				<td>200</td>
 			</tr>

mrcImageCTFDetermination - Revision history

Kinoshita at 07:29, 1 October 2014

Kinoshita at 07:29, 1 October 2014

Kinoshita: /* Main option */

Kinoshita: /* List of option */

Kinoshita: /* Main option */

Kinoshita: /* Main option */