mrcImageCTFCompensation

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mrcImageCTFCompensation is Eos's Command that corrects CTF (Contrast Transfer Function) for mrcImage files taken by a transmission electron microscope.

List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage(FFT) stdin
-o Essential Output: mrcImage stdout
-info Optional CTF information: ASCII NULL
-info2 Optional CTF information2: ASCII NULL
-kV Optional Acceleration voltage[kV] 200
-Cs Optional Spherical aberration coefficient[mm] 2.1
-df Optional Defocus(under is +): [A] 27000
-white Optional WhiteNoise(Noise/Signal) 0.1
-SinWin Optional Windowing by sine function from Rmin[/A] to Rmax[/A].Default: No Window.: (SinWinRmin, SinWinRmax) 補正なし
-A Optional The ratio of amplitude contrast to phase contrast(Amplitude/Phase) 0.1
-Astig Optional With Astigmatism (difMin, dfMax, asAxis)) (0, 0 , 0)
-NoAstig Optional Without Astigmatism
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help  
If you set -NoAstig, -Astig, -Info2 are ignored.


-m details

Value Description
0 No Correction
1 x ctf/|ctf| phase flipping
2 x ctf phase flipping and ctf-multiplying
3 x 1/ctf (0.1<|ctf| ) phase flipping and ctf-divided
4 x ctf/(SQR(ctf)+SQR(NS)) phase-flipping + Winner Filtering
5 x SQR(ctf) x ctf/|ctf| phase-flipping + ctf-Weighted
6 x 1/|ctf| (0.1<|ctf|) No phase-flipping + ctf-divided
7 x |ctf|/(SQR(ctf)+SQR(NS)) No phase flipping + Winner Filtering
8 x ctf /(SQR(ctf)+SQR(NS*exp(a*R))) phase flipping + Winner Filtering + NS-raising
9 x |ctf|/(SQR(ctf)+SQR(NS*exp(a*R))) No phase flipping + Winner Filtering + NS-raising


-info format

defocus Cs kV AmplitudeContrast
By llExtractWithLayerSeparationFilamentInfo(-oI)


-info2 format

By ctfDisplay(-o) or Display2


Execution example

Input file image

Input-B120-CTF.png

Min

Max
Mean
SD

SE

0.000514398 (78, 51, 0)

1684.3 (0, 0, 0)
9.67542
65.3969

0.817461


-info data

CTF information
27000.000000 2.100000 200.000000 0.100000


-info2 のデータ

CTF information2
...

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

...


Example of options only essential

Outdata-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-298.592 (37, 36, 0)

46.4642 (56, 19, 0)
-21.0538
52.1224

0.65153


Option -m

Case: m=1, kV=200

Case: No other settings
Outdata-m1kV-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

0 (0, 0, 0)
0
0

0


Case: info=CTF information
Outdata-m1info-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-38.9125 (41, 61, 0)

268.151 (39, 35, 0)
21.0538
52.1224

0.65153


Case: info2=CTF information2
Outdata-m1info2-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-38.9125 (41, 61, 0)

268.151 (39, 35, 0)
21.0538
52.1224

0.65153


Case: Cs=2.1
Outdata-m1Cs-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-277.543 (37, 36, 0)

67.5181 (56, 19, 0)
-1.29646e-08
52.1224

0.65153


Case: df=27000
Outdata-m1df-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-59.6211 (51, 54, 0)

244.573 (39, 35, 0)
1.41363e-08
52.1224

0.65153


Case: A=0.1
Outdata-m1A-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-46.4642 (56, 19, 0)

298.592 (37, 36, 0)
21.0538
52.1224

0.65153


Case: Astig=(2000, 3000, 30)
Outdata-m1Astig-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-63.7102 (56, 19, 0)

278.233 (37, 35, 0)
-2.56419e-07
52.1224

0.65153


Case: m=2, info=CTF information

Outdata-m2-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-62.4959 (28, 30, 0)

115.688 (39, 34, 0)
2.10538
20.8081

0.260101


Case: m=3, info=CTF information

Outdata-m3-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-49.5112 (2, 15, 0)

1120.94 (39, 39, 0)
210.538
256.745

3.20931


Case: m=4, info=CTF information

Case: No other settings
Outdata-m4-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-76.6069 (1, 16, 0)

835.557 (40, 39, 0)
105.269
192.376

2.4047


Case: white=0.5
Outdata-m4white-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-59.6252 (50, 54, 0)

195.105 (39, 35, 0)
8.0976
38.5767

0.482208


Case: m=5, info=CTF information

Outdata-m5-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-63.7521 (29, 30, 0)

81.6286 (39, 34, 0)
0.210538
16.0662

0.200828


Case: m=6, info=CTF information

Outdata-m6-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-1338.09 (37, 36, 0)

212.611 (2, 70, 0)
-210.538
272.238

3.40297


Case: m=7, info=CTF information

Case: No other settings
Outdata-m7-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-885.311 (37, 36, 0)

43.1237 (2, 0, 0)
-105.269
192.376

2.4047


Case: white=0.5
Outdata-m7white-mrcImageCTFCompensation.png

Min

Max
Mean
SD

SE

-221.279 (37, 36, 0)

60.2085 (29, 27, 0)
-8.0976
38.5767

0.482208