Testing the Scanner

How we tested the Zeiss SCAI Scanner for use with EM negatives

OD range 0.1-1.4
Linearity 0%
No color correction
Monochrome mode
Zeiss proprietary lookup table (LUT)

  • Scan image of EM grid provided by Richard Henderson at 7um interval
  • LD2MRC or TIF2MRC to convert to MRC format
  • Ximdisp (or LABEL) to select area 512x512 pixels
  • FFTRANS to calculate fft of selected area
  • LABEL (option 5) to output intensities from fft
  • Ximdisp to display intensities

Choose "average boxed densities"
Draw box around each spot along x direction and around background near each spot
Same for y direction

  • Calculate integrated amplitude for each reflection

integrated amp = sqrt( (measured avg intensity - bkg avg intensity) *
num of pixels)
e.g., in above image, 1 listed spot (1st order x direction) would be:
222.17 = sqrt( ( 57.72-0.59)*864)

  • Finally, calculate ratio of 2nd, 3rd, 4th order spots relative to
    1st order spot in both x and y direction

Values calculated at various times on various scanners all from copies of this image
10/28/99  Our scanner immediately after installation

order        lowerleft          
lowerright           
middle

x       
y             
x       y           
x        y

1      1.0     
1.0            1.0    
1.0          1.0     
1.0

2      0.384    0.415         
0.375   0.407        0.379   
0.410

3      0.0738   0.0964        
0.0695  0.0911       0.0720  
0.0943

4      0.0363   0.0335        
0.0347  0.0310       0.0358  
0.319

order        upperleft          
upperright

x       
y             
x       y

1      1.0     
1.0            1.0    
1.0

2      0.383    0.417         
0.371   0.405

3      0.0746   0.0987        
0.0680  0.0910

4      0.0367   0.0356        
0.0345  0.0360

9/28/99  Our scanner at factory (by Klaus Neumann)

order        lowerleft          
lowerright           
middle

x       
y             
x       y           
x        y

1      1.0     
1.0            1.0    
1.0          1.0     
1.0

2      0.398    0.434         
0.370   0.410        0.388   
0.422

3      0.887    0.114         
0.710   0.098        0.0816  
0.107

4      0.0287   0.0282        
0.0247  0.0250       0.0284  
0.0290

order        upperleft          
upperright

x       
y             
x       y

1      1.0     
1.0            1.0    
1.0

2      0.390    0.427         
0.383   0.416

3      0.0831   0.108         
0.0785  0.103

4      0.0281   0.0282        
0.0251  0.0269

7/16/99  (from Klaus Neumann - 2 different focusses)

order  scan001x scan001y    scan002x 
scan002y

(emgrid1)            
(emgrid2)

1      1.0     
1.0           1.0     
1.0

2      0.40    
0.436         0.31    
0.333

3      0.086    0.114        
0.040    0.054

4      0.025    0.026        
0.015    0.017

7/22/99  (followup to Gordon Conf)

order        lowerleft          
lowerright           
middle

x       
y             
x       y           
x        y

1      1.0     
1.0            1.0    
1.0          1.0     
1.0

2      0.396    0.428         
0.387   0.428        0.380   
0.412

3      0.086    0.111         
0.080   0.110        0.0764  
0.100

4      0.027    0.027         
0.0277  0.0298       0.0258  
0.0260

order        upperleft          
upperright

x       
y             
x       y

1      1.0     
1.0            1.0    
1.0

2      0.397    0.426         
0.398   0.432

3      0.086    0.110         
0.0867  0.107

4      0.0262   0.0250        
0.0278  0.0273

7/10/99  PDS1010GM (NYU) (same data as previously provided)

x        
y

1       1.0      
1.0

2       0.488    
0.490

3       0.114    
0.143

4       0.048    
0.040