mrcImageSimilarityEstimate

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mrcImageSimilarityEstimate is Eos's Command.


List of option

Main option

Option Essential/Optional Description Default
-i Essential Input: mrcImage(FFT) NULL
-o Optional Output: ASCII NULL
-oCor Optional Output: mrcImage NULL
-ref Essential Reference file list: ASCII stdin
-corfilename Optional Correlation file list: ASCII stdin
-cormode Optional cormode 0
-ctfinfo Optional CTF Information: ASCII NULL
-c Optional ConfigurationFile NULL
-m Optional Mode 0
-h Optional Help 　
-o, -ctfinfo is required.
It must be the same number of files about -corfilename and -ref.


-m details

Value Description
0


-cormode details

Value Description
0 Normal Correlation FxG*
1 Phase Correlation FxG*/ |FxG*|
2 Phase Correlation FxG*/sqrt(|FxG*|)
3 Normalized Normal Correlation FxG*/|F||G|)
16 (0, 0)=0


-ref format

2Dfile1
2Dfile2
.
.


-ctfinfo format

defocus Cs kV AmplitudeContrast


Execution example

Input file image

Input-1VOM-N-Rot3-2D-FFT.png
By mrcFFTExpression(m=1)

Min

Max
Mean
SD

SE

57.2237 (78, 32, 0)

520564 (0, 0, 0)
4898.64
12077.5

150.969


Reference file data

Input-1VOM-2D.mrc
Input-1VOM-Rot-2D.mrc
Input-1VOM-Rot1-2D.mrc
Input-1VOM-Rot2-2D.mrc
Input-1VOM-Rot3-2D.mrc
Input-1VOM-Rot4-2D.mrc


Input-1VOM-2D.mrc's image
Input-1VOM-2D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

49749.7 (27, 28, 0)
7212.9
8827.15

110.339


Input-1VOM-Rot-2D.mrc's image
Input-1VOM-Rot-2D.png

Min

Max
Mean
SD

SE

-609.552 (68, 18, 0)

43476 (45, 47, 0)
6507.15
7376.01

92.2001


Input-1VOM-Rot1-2D.mrc's image
Input-1VOM-Rot1-2D.png

Min

Max
Mean
SD

SE

-2.31309e-06 (29, 7, 0)

49749.2 (52, 51, 0)
6572.32
8769.91

109.624


Input-1VOM-Rot2-2D.mrc's image
Input-1VOM-Rot2-2D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

49749.2 (28, 52, 0)
6572.32
8769.91

109.624


Input-1VOM-Rot3-2D.mrc's image
Input-1VOM-Rot3-2D.png

Min

Max
Mean
SD

SE

-1.70846e-06 (56, 57, 0)

40287.6 (43, 43, 0)
6509.38
8494.21

106.178


Input-1VOM-Rot4-2D.mrc's image
Input-1VOM-Rot4-2D.png

Min

Max
Mean
SD

SE

0 (0, 0, 0)

40287.6 (43, 36, 0)
6509.38
8494.21

106.178


Option -ctfinfo

Using following data
27000.000000 2.100000 200.000000 0.100000


Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 0 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max 594983936.000000 (      31.000000       39.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max: 594983936.000000 (      31.000000,       39.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max: 416067136.000000 (      19.000000,       26.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max: 693353536.000000 (      52.000000,       44.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max: 701726912.000000 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max: 730086528.000000 (      28.000000,       29.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max: 844069504.000000 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       5.000000 max:844069504.000000 (      33.000000,       41.000000,        0.000000) correlation mode 0 in main


-o's data
Input-1VOM-N-Rot3-2D.fft maxNumber:        5.000000 max: 844069504.000000 (      33.000000,       41.000000,        0.000000) correlation mode 0


In the following, Setting at-ctfinfo.

Option -oCor

-oCor 's image
Outdata-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.41115e+09 (3, 78, 0)

8.4407e+08 (33, 41, 0)
-3.38855e+08
5.16823e+08

6.46029e+06
Correlation of last Reference file


Option -corfilename

Using following data
Cor.mrc
Cor-Rot.mrc
Cor-Rot1.mrc
Cor-Rot2.mrc
Cor-Rot3.mrc
Cor-Rot4.mrc


Cor.mrc's image
Outdata1-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.78706e+09 (1, 0, 0)

5.94984e+08 (31, 39, 0)
-3.75478e+08
5.55949e+08

6.94936e+06


Cor-Rot.mrc's image
Outdata2-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.96178e+09 (0, 0, 0)

4.16067e+08 (19, 26, 0)
-3.38739e+08
5.38895e+08

6.73619e+06


Cor-Rot1.mrc's image
Outdata3-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.84834e+09 (2, 2, 0)

6.93354e+08 (52, 44, 0)
-3.42132e+08
5.72357e+08

7.15446e+06


Cor-Rot2.mrc's image
Outdata4-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.78266e+09 (6, 3, 0)

7.01727e+08 (33, 41, 0)
-3.42132e+08
6.59549e+08

8.24436e+06


Cor-Rot3.mrc's image
Outdata5-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.83911e+09 (78, 77, 0)

7.30087e+08 (28, 29, 0)
-3.38855e+08
5.96151e+08

7.45189e+06


Cor-Rot4.mrc's image
Outdata6-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.41115e+09 (3, 78, 0)

8.4407e+08 (33, 41, 0)
-3.38855e+08
5.16823e+08

6.46029e+06
Last image is same to -oCor.


Option -cormode

Case: cormode=1

Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 1 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max        3.320063 (      60.000000       55.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max:        3.320063 (      60.000000,       55.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max:        3.700860 (      75.000000,       26.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max:        3.524074 (      10.000000,       58.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max:        4.016609 (      36.000000,       74.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max:        3.594912 (      71.000000,       37.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max:        4.224592 (      63.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       5.000000 max:       4.224592 (      63.000000,       41.000000,        0.000000) correlation mode 1 in main


-oCor 's image
Outdata-m1-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-3.71458 (8, 56, 0)

4.22459 (63, 41, 0)
-0.0125
0.999922

0.012499


Case: cormode=2

Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 2 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max    14465.583984 (      32.000000       32.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max:    14465.583984 (      32.000000,       32.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max:    13782.997070 (      34.000000,       34.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max:    14514.052734 (      49.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max:    17554.871094 (      38.000000,       27.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max:    18164.224609 (      31.000000,       28.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max:    16113.549805 (      32.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       4.000000 max:   18164.224609 (      31.000000,       28.000000,        0.000000) correlation mode 2 in main


-oCor 's image
Outdata-m２-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-20418.3 (76, 79, 0)

18164.2 (31, 28, 0)
-2058.08
5706.55

71.3319


Case: cormode=3

Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 3 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max        0.019808 (      31.000000       39.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max:        0.019808 (      31.000000,       39.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max:        0.015354 (      19.000000,       26.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max:        0.025332 (      52.000000,       44.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max:        0.025638 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max:        0.026932 (      28.000000,       29.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max:        0.031137 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       5.000000 max:       0.031137 (      33.000000,       41.000000,        0.000000) correlation mode 3 in main


-oCor 's image
Outdata-m3-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-0.052056 (3, 78, 0)

0.0311368 (33, 41, 0)
-0.0125
0.0190651

0.000238313


Case: cormode=16

Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 16 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max 970461568.000000 (      31.000000       39.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max: 970461568.000000 (      31.000000,       39.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max: 754806144.000000 (      19.000000,       26.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max: 1035485184.000000 (      52.000000,       44.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max: 1043858560.000000 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max: 1068941312.000000 (      28.000000,       29.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max: 1182924416.000000 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       5.000000 max:1182924416.000000 (      33.000000,       41.000000,        0.000000) correlation mode 16 in main


-oCor 's image
Outdata-m16-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-1.0723e+09 (3, 78, 0)

1.18292e+09 (33, 41, 0)
-1.14038
5.16823e+08

6.46029e+06


Case: cormode=17

Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 17 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max        3.332563 (      60.000000       55.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max:        3.332563 (      60.000000,       55.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max:        3.713360 (      75.000000,       26.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max:        3.536574 (      10.000000,       58.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max:        4.029109 (      36.000000,       74.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max:        3.607412 (      71.000000,       37.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max:        4.237092 (      63.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       5.000000 max:       4.237092 (      63.000000,       41.000000,        0.000000) correlation mode 17 in main


-oCor 's image
Outdata-m17-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-3.70208 (8, 56, 0)

4.23709 (63, 41, 0)
-2.11159e-10
0.999922

0.012499


Case: cormode=18

Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 18 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max    16632.027344 (      32.000000       32.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max:    16632.027344 (      32.000000,       32.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max:    15840.724609 (      34.000000,       34.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max:    16582.058594 (      49.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max:    19622.876953 (      38.000000,       27.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max:    20222.302734 (      31.000000,       28.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max:    18171.628906 (      32.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       4.000000 max:   20222.302734 (      31.000000,       28.000000,        0.000000) correlation mode 18 in main


-oCor 's image
Outdata-m18-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-18360.3 (76, 79, 0)

20222.3 (31, 28, 0)
2.73261e-06
5706.55

71.3319


Case: cormode=19

Output
Cs        2.100000, defocus    27000.000000, kV      200.000000, mode 1, AoverP        0.100000, Ain        0.000000 in main 
Image Number 6 in main
correlation mode: 19 in lmrcImageSimilarityEstimate
maxNumber        0.000000, max        0.032308 (      31.000000       39.000000        0.000000) in lmrcImageSimilarityEstimate
i: 0, max:        0.032308 (      31.000000,       39.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 1, max:        0.027854 (      19.000000,       26.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 2, max:        0.037832 (      52.000000,       44.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 3, max:        0.038138 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 4, max:        0.039432 (      28.000000,       29.000000,        0.000000) in lmrcImageSimilarityEstimate
i: 5, max:        0.043637 (      33.000000,       41.000000,        0.000000) in lmrcImageSimilarityEstimate
maxNumber:       5.000000 max:       0.043637 (      33.000000,       41.000000,        0.000000) correlation mode 19 in main


-oCor 's image
Outdata-m19-mrcImageSimilarityEstimate.png

Min

Max
Mean
SD

SE

-0.039556 (3, 78, 0)

0.0436368 (33, 41, 0)
2.04503e-11
0.0190651

0.000238313


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