Difference: TecnaiInformation (24 vs. 25)

Revision 2511 Mar 2015 - Main.BillRice

 
META TOPICPARENT name="CryoEM"

FEI TF20 Microscope Parameters

wavelengths

* 200kV: 0.02508 A

objective lenses

  • f=
  • Cs = 2.1 mm
  • Chromatic aberration =

Aperture Sizes

Changed:
<
<
  • Condensor : 150 um, 70 um, 50 um, 50 um
  • Objective : 50 um, 50 um, 50 um, 40 um
>
>
  • Condensor : 150 um, 100 um, 50 um, 50 um
    • Have used 70 um aperture, removed 03-06-15, could be put back in
Added:
>
>
  • Objective : 100 um, 50 um, 50 um, 40 um
    • have 2 spare 100 um apertures 03-06-15
 
  • Selected Area: 200 um, 100 um, 70 um, 40 um

CCD information

Added:
>
>
  • Tietz F416; installed Jan 2015
 
  • Size of camera : 4096 x 4096 pixels
Changed:
<
<
  • Pixel size: 15 um
  • Post-film mag : 1.76
  • Gain in SerialEM : 29 counts / electron
  • Gain in EM Menu3: 14.5 counts / electron
>
>
  • Pixel size: 15.6 um
  • Post-film mag : 1.76 OLD CAMERA
  • Gain: 24 counts / electron

 
Changed:
<
<

CCD : Signal to noise ratio in comparison to film

>
>

CCD : Signal to noise ratio in comparison to film OLD CAMERA NO LONGER RELEVANT

 
  • SNR of tecnai CCD:
    tecnai-ccd.png
  • SNR -tecnai film:
    tecnai-film.png

Magnification Calibration: Tecnai F20

  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Added:
>
>
  • Tietz F416 -- done 03-11-2015
 
Set Magnification (screen up) CCD Magnification Unbinned Pixel Size (A) 2X Binned Pixel Size (A) Tilt Axis Angle calibrated film mag
Changed:
<
<
2100 (LM) 3,624 41.4 110 -80.2  
1,700 2,977 50.4 100.8 90.8  
2,500 4,403 34.1 68.1 90.9  
3,500 6,037 24.8 49.7 91.8  
5,000 8,938 16.78 33.6 91.3  
6,500 11,467 13.08 26.2 91.2  
7,800 13,824 10.85 21.7 91.1  
9,600 17,088 8.78 17.56 91.1  
11,500 20,348 7.37 14.74 91.0  
14,500 25,857 5.80 11.60 90.8  
19,000 33,904 4.42 8.85 91.0  
25,000 42,611 3.52 7.04 90.9  
29,000 50,592 2.96 5.93 90.8  
50,000 88,249 1.700 3.40 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.378 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.073 2.15 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 1.11 ND gold lattice
200,000 357,100 0.420 0.840 ND gold lattice
240,000 427,400 0.351 0.702 ND gold lattice
280,000 505,100 0.297 0.594 ND gold lattice
390,000 694,400 0.216 0.432 ND gold lattice
490,000 862,100 0.174 0.348 ND gold lattice
700,000 1.250M 0.120 0.240 ND gold lattice
>
>
2100 (LM) 3,624 41.7 83.4 -88  
1,700 2,977 50.7 101.4 74.4  
2,500 4,403 34.4 68.8 90.9  
3,500 6,037 25.0 50.0 91.8  
5,000 8,938 16.8 33.6 91.3  
6,500 11,467 13.0 26.0 91.2  
7,800 13,824 10.8 21.6 91.1  
9,600 17,088 8.80 17.6 91.1  
11,500 20,348 7.55 15.10 91.0  
14,500 25,857 5.91 11.82 90.8  
19,000 33,904 4.46 8.92 91.0  
25,000 42,611 3.56 7.04 90.9  
29,000 50,592 2.99 5.98 90.8  
50,000 88,249 1.71 3.42 92.4 51,190 +/- 90 (n=13) 51,787 +/- 90 at 120kV (n=14)
62,000 108,857 1.39 2.76 92.4 63,410 +/- 104 (n=12) 63,735 +/- 160 at 120kV (n=10)
80,000 139,813 1.07 2.14 92.4 81,190 +/- 111 (n=4)
150,000 270,800 0.554 ND 1.11 ND gold lattice
200,000 357,100 0.420 ND 0.840 ND gold lattice
240,000 427,400 0.351 ND 0.702 ND gold lattice
280,000 505,100 0.297 ND 0.594 ND gold lattice
390,000 694,400 0.216 ND 0.432 ND gold lattice
490,000 862,100 0.174 ND 0.348 ND gold lattice
700,000 1.250M 0.120 ND 0.240 ND gold lattice
 
Changed:
<
<
  • Average CCD to film factor: 1.76
>
>
  • Average CCD to film factor:
 
  • fim mags calibrated using negative-stain TMV, measuring height of layer line at 23A
Changed:
<
<

Magnification Calibration: Tecnai F20 at 120kV

>
>

Magnification Calibration: Tecnai F20 at 120kV OLD CAAMERA OBSOLETE

 
  • Magnifications calibrated using 2160 cross grid using method described in SerialEM documentation
Set Magnification (screen up) Unbinned Pixel Size (A)
1,100 77.5
1,500 55.6
1,700 48.1
2,100 39.1
2,500 32.5
3,500 23.9
5,000 16.1
6,500 12.4
7,800 10.3
9,600 8.36
11,500 7.15
14,500 5.67
19,000 5.12
25,000 3.45
29,000 2.87
Changed:
<
<

Defocus Offset for Low dose mode

>
>

Defocus Offset for Low dose mode OLD CAMERA

 
  • Calculated May 6 2013, df range 500 nm to 3500 nm
  • line of best fit: df = 1.12* set_df + 800nm
  • Data collected using Focus at 250000X, Exposure at 50000X, spot 4
  • Quantifoil carbon grid. Defocus calculated using ctffind3 software
  • Plot of df offset data:
    f20_defocus_offset.png

* tf20_df2.txt: raw data defocus calcs

  • Calculated Nov 29 2013, df range: -500 nm to 3000 nm
  • Data collected using Focus at 280,000X, Exposure at 25,000X, spot 5, and Exposure at 50,000X, spot 5, and
  • Carbon grid, nickel grid, Borate tubes negatively stained (with uranyl acetate). Defocus calculated using ctffind3 software
  • Plots of df offset data:

* x25,000: line of best fit: df = 1.02* set_df + 0.8 um
x25Curve_131202.jpg

* x50,000: line of best fit: df = 1.04* set_df + 0.92 um
x50Curve_131202.jpg

Defocus Offset for Low dose mode at 120 kV

Changed:
<
<
April 4, 2014
>
>
April 4, 2014 OLD CAMERA
 
  • line of best fit: df = 1.15* set_df + 1139nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, defocus sets taken: 5 images at 0, then 5 at 500 nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140320-tf20-120kV.jpg

March 27, 2014
  • Calculated March 27 2014, df range 0 nm to 3500 nm
  • line of best fit: df = 1.14* set_df + 503nm
  • Data collected using Focus at 200000X, Exposure at 50000X, spot 5, cycled through exposure, search, focus and exposure for each micrograph, defocus series taken: 0, 500 nm, 1000nm, etc...
  • Defocus calculated using ctffind3 software
  • plot of tf20 df offset at 120 keV:
    20140318-tf20-120kV.jpg
Changed:
<
<

Leginon: Goniometer model

>
>

Leginon: Goniometer model OLD CAMERA

 
  • X axis
xcal2.png

  • Y axis
ycal.png

  • Set ALLOWTOPICVIEW =

-- BillRice - 28 Sep 2007

* filmcal.zip: film calibrations 200kv

* filmcal_tecnai_2011.zip: film calibrations 200kv

META FILEATTACHMENT attr="" autoattached="1" comment="leginon stage y cal" date="1207331150" name="ycal.png" path="ycal.png" size="10924" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="raw data defocus calcs" date="1368041535" name="tf20_df2.txt" path="tf20_df2.txt" size="1804" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996178" name="x50Curve_131202.jpg" path="x50Curve_131202.jpg" size="18928" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of df offset data" date="1368041497" name="f20_defocus_offset.png" path="f20_defocus_offset.png" size="5711" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="leginon x-stage cal" date="1207331127" name="xcal2.png" path="xcal2.png" size="9105" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="" date="1385996170" name="x25Curve_131202.jpg" path="x25Curve_131202.jpg" size="19120" user="Main.NicolasCoudray" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="SNR of tecnai CCD" date="1190995417" name="tecnai-ccd.png" path="tecnai-ccd.png" size="367827" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396624753" name="20140320-tf20-120kV.jpg" path="20140320-tf20-120kV.jpg" size="26523" user="Main.EdEng" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="snr -tecnai film" date="1190995549" name="tecnai-film.png" path="tecnai-film.png" size="462385" user="Main.BillRice" version=""
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315419720" name="filmcal.zip" path="filmcal.zip" size="431408778" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="film calibrations 200kv" date="1315428187" name="filmcal_tecnai_2011.zip" path="filmcal_tecnai_2011.zip" size="42304028" user="Main.BillRice" version="1"
META FILEATTACHMENT attr="" autoattached="1" comment="plot of tf20 df offset at 120 keV" date="1396037567" name="20140318-tf20-120kV.jpg" path="20140318-tf20-120kV.jpg" size="31666" user="Main.EdEng" version="1"
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