Difference: CcdCalculations (1 vs. 8)

Revision 811 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
  • Set beam intensity to 1 second exposure time
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
  • From CCD calibration, convert square nm to pixels, get dose in electrons/pixel
  • Gain = counts per pixel / electrons per pixel = counts per electron

Tabulated data

Magnification Dose (e/nm^2) nm/pixel Dose (e/pixel) Counts/pixel Gain
5800 7.298 1.308 39.4 1151.3 29.2
19000 199.2155 0.442 38.92 1169.99 30.06
25000 342.9676 0.352 42.5 1162.54 27.36
29000 448.6993 0.296 39.31 1134.07 28.85
50000 1418.9582 .170 41.0 1205.6 29.40
Changed:
<
<
>
>
  • NOTE: Counts in SerialEM are 2* counts in EM Menu3, gain 0
 

Jeol 2100F

Procedure

  • 50K Mag, spot 5, set intensity to 10 pA/cm^2 (small screen)
  • Set gain on CCD to desired level
  • Insert and center SA Aperture #3; beam should now fully fit on small screen
  • Read screen current on small screen in pA/cm^2
  • Take a 1 second Exposure image
Changed:
<
<
  • Using ImageJ? software, box out area inside exposed circle and measure average counts, sd
>
>
  • Using ImageJ software, box out area inside exposed circle and measure average counts, sd
 
  • Determine pixel area covered by SA aperture as follows:
    1. import image into spider
Changed:
<
<
    1. Using th m command, threshold at level of (mean - 5 standard deviations)
>
>
    1. Using th m command, threshold at level of (mean - 5 standard deviations)
 
    1. Using Hi T command, measure average of thresholded mask calculated above
    2. Pixel Area = 2048*2048*avg intensity
  • Total counts = Avg counts * pixel area
  • Convert current to electrons as follows:
    1. Diameter of small screen = 2.5 cm - > area = 4.91 cm^2
    2. 1 sec exposure means 1 Coulomb per Ampere
    3. 1 elecron = 1.60 * 10^-19 C
    4. Electrons = (pA/cm^2 * 4.91 cm^2 )/ (1.6*10^-7 e/pA)
  • Gain = total counts/total electrons

  • area of SA #3: 1.16 * 10^6 pixels

Tabulated Data

Trial Mean Counts Total Counts Current (pA/cm^2) Electrons Gain (counts/electron)
Low 1 2896.8 3.36 *10^9 2.5 7.67 * 10^7 43.8
Low 2 2902.2 3.37 * 10^9 2.5 7.67 * 10^7 43.9
Low 3 2984.3 3.46 * 10^ 9 2.5 7.67 * 10^7 45.1
Low 4 2977.1 3.45 * 10 ^9 2.5 7.67 *10^7 45.0
High 1 11780 1.37 * 10^10 2.5 7.67 * 10^7 178
High 2 11750 1.36 * 10^10 2.5 7.67 *10^7 178

JEOL 3200FSC

Procedure

  • Similar to Jeol 2100F, but use SA aperture 3 and Entrance aperture 3

Tabulated Data

Aperture Area Avg counts Total Counts Current (pA/cm^2) Electrons Gain
EA 3 3.50 * 10^6 614.524 2.15 * 10^9 2.45 7.52 * 10^7 28.6
SA 3 3.48 * 10^6 614.294 2.14 * 10^9 2.40 7.36 * 10^7 29.1

  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

Revision 711 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
  • Set beam intensity to 1 second exposure time
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
  • From CCD calibration, convert square nm to pixels, get dose in electrons/pixel
  • Gain = counts per pixel / electrons per pixel = counts per electron

Tabulated data

Magnification Dose (e/nm^2) nm/pixel Dose (e/pixel) Counts/pixel Gain
5800 7.298 1.308 39.4 1151.3 29.2
19000 199.2155 0.442 38.92 1169.99 30.06
25000 342.9676 0.352 42.5 1162.54 27.36
Changed:
<
<
29000 448.6993   39.31 1134.07 28.85
>
>
29000 448.6993 0.296 39.31 1134.07 28.85
 
50000 1418.9582 .170 41.0 1205.6 29.40

Jeol 2100F

Procedure

  • 50K Mag, spot 5, set intensity to 10 pA/cm^2 (small screen)
  • Set gain on CCD to desired level
  • Insert and center SA Aperture #3; beam should now fully fit on small screen
  • Read screen current on small screen in pA/cm^2
  • Take a 1 second Exposure image
  • Using ImageJ? software, box out area inside exposed circle and measure average counts, sd
  • Determine pixel area covered by SA aperture as follows:
    1. import image into spider
    2. Using th m command, threshold at level of (mean - 5 standard deviations)
    3. Using Hi T command, measure average of thresholded mask calculated above
    4. Pixel Area = 2048*2048*avg intensity
  • Total counts = Avg counts * pixel area
  • Convert current to electrons as follows:
    1. Diameter of small screen = 2.5 cm - > area = 4.91 cm^2
    2. 1 sec exposure means 1 Coulomb per Ampere
    3. 1 elecron = 1.60 * 10^-19 C
    4. Electrons = (pA/cm^2 * 4.91 cm^2 )/ (1.6*10^-7 e/pA)
  • Gain = total counts/total electrons

  • area of SA #3: 1.16 * 10^6 pixels

Tabulated Data

Trial Mean Counts Total Counts Current (pA/cm^2) Electrons Gain (counts/electron)
Low 1 2896.8 3.36 *10^9 2.5 7.67 * 10^7 43.8
Low 2 2902.2 3.37 * 10^9 2.5 7.67 * 10^7 43.9
Low 3 2984.3 3.46 * 10^ 9 2.5 7.67 * 10^7 45.1
Low 4 2977.1 3.45 * 10 ^9 2.5 7.67 *10^7 45.0
High 1 11780 1.37 * 10^10 2.5 7.67 * 10^7 178
High 2 11750 1.36 * 10^10 2.5 7.67 *10^7 178

JEOL 3200FSC

Procedure

  • Similar to Jeol 2100F, but use SA aperture 3 and Entrance aperture 3

Tabulated Data

Aperture Area Avg counts Total Counts Current (pA/cm^2) Electrons Gain
EA 3 3.50 * 10^6 614.524 2.15 * 10^9 2.45 7.52 * 10^7 28.6
SA 3 3.48 * 10^6 614.294 2.14 * 10^9 2.40 7.36 * 10^7 29.1

  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

Revision 611 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
  • Set beam intensity to 1 second exposure time
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
  • From CCD calibration, convert square nm to pixels, get dose in electrons/pixel
  • Gain = counts per pixel / electrons per pixel = counts per electron

Tabulated data

Magnification Dose (e/nm^2) nm/pixel Dose (e/pixel) Counts/pixel Gain
5800 7.298 1.308 39.4 1151.3 29.2
Changed:
<
<
19000 199.2155   38.92 1169.99 30.06
>
>
19000 199.2155 0.442 38.92 1169.99 30.06
 
25000 342.9676 0.352 42.5 1162.54 27.36
29000 448.6993   39.31 1134.07 28.85
50000 1418.9582 .170 41.0 1205.6 29.40

Jeol 2100F

Procedure

  • 50K Mag, spot 5, set intensity to 10 pA/cm^2 (small screen)
  • Set gain on CCD to desired level
  • Insert and center SA Aperture #3; beam should now fully fit on small screen
  • Read screen current on small screen in pA/cm^2
  • Take a 1 second Exposure image
  • Using ImageJ? software, box out area inside exposed circle and measure average counts, sd
  • Determine pixel area covered by SA aperture as follows:
    1. import image into spider
    2. Using th m command, threshold at level of (mean - 5 standard deviations)
    3. Using Hi T command, measure average of thresholded mask calculated above
    4. Pixel Area = 2048*2048*avg intensity
  • Total counts = Avg counts * pixel area
  • Convert current to electrons as follows:
    1. Diameter of small screen = 2.5 cm - > area = 4.91 cm^2
    2. 1 sec exposure means 1 Coulomb per Ampere
    3. 1 elecron = 1.60 * 10^-19 C
    4. Electrons = (pA/cm^2 * 4.91 cm^2 )/ (1.6*10^-7 e/pA)
  • Gain = total counts/total electrons

  • area of SA #3: 1.16 * 10^6 pixels

Tabulated Data

Trial Mean Counts Total Counts Current (pA/cm^2) Electrons Gain (counts/electron)
Low 1 2896.8 3.36 *10^9 2.5 7.67 * 10^7 43.8
Low 2 2902.2 3.37 * 10^9 2.5 7.67 * 10^7 43.9
Low 3 2984.3 3.46 * 10^ 9 2.5 7.67 * 10^7 45.1
Low 4 2977.1 3.45 * 10 ^9 2.5 7.67 *10^7 45.0
High 1 11780 1.37 * 10^10 2.5 7.67 * 10^7 178
High 2 11750 1.36 * 10^10 2.5 7.67 *10^7 178

JEOL 3200FSC

Procedure

  • Similar to Jeol 2100F, but use SA aperture 3 and Entrance aperture 3

Tabulated Data

Aperture Area Avg counts Total Counts Current (pA/cm^2) Electrons Gain
EA 3 3.50 * 10^6 614.524 2.15 * 10^9 2.45 7.52 * 10^7 28.6
SA 3 3.48 * 10^6 614.294 2.14 * 10^9 2.40 7.36 * 10^7 29.1

  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

Revision 511 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
  • Set beam intensity to 1 second exposure time
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
  • From CCD calibration, convert square nm to pixels, get dose in electrons/pixel
  • Gain = counts per pixel / electrons per pixel = counts per electron

Tabulated data

Magnification Dose (e/nm^2) nm/pixel Dose (e/pixel) Counts/pixel Gain
5800 7.298 1.308 39.4 1151.3 29.2
19000 199.2155   38.92 1169.99 30.06
25000 342.9676 0.352 42.5 1162.54 27.36
29000 448.6993   39.31 1134.07 28.85
50000 1418.9582 .170 41.0 1205.6 29.40

Jeol 2100F

Procedure

  • 50K Mag, spot 5, set intensity to 10 pA/cm^2 (small screen)
  • Set gain on CCD to desired level
  • Insert and center SA Aperture #3; beam should now fully fit on small screen
  • Read screen current on small screen in pA/cm^2
  • Take a 1 second Exposure image
  • Using ImageJ? software, box out area inside exposed circle and measure average counts, sd
  • Determine pixel area covered by SA aperture as follows:
    1. import image into spider
    2. Using th m command, threshold at level of (mean - 5 standard deviations)
    3. Using Hi T command, measure average of thresholded mask calculated above
    4. Pixel Area = 2048*2048*avg intensity
  • Total counts = Avg counts * pixel area
  • Convert current to electrons as follows:
    1. Diameter of small screen = 2.5 cm - > area = 4.91 cm^2
    2. 1 sec exposure means 1 Coulomb per Ampere
    3. 1 elecron = 1.60 * 10^-19 C
    4. Electrons = (pA/cm^2 * 4.91 cm^2 )/ (1.6*10^-7 e/pA)
  • Gain = total counts/total electrons

  • area of SA #3: 1.16 * 10^6 pixels
Changed:
<
<

Tabulated Results

>
>

Tabulated Data

 
Trial Mean Counts Total Counts Current (pA/cm^2) Electrons Gain (counts/electron)
Low 1 2896.8 3.36 *10^9 2.5 7.67 * 10^7 43.8
Low 2 2902.2 3.37 * 10^9 2.5 7.67 * 10^7 43.9
Low 3 2984.3 3.46 * 10^ 9 2.5 7.67 * 10^7 45.1
Low 4 2977.1 3.45 * 10 ^9 2.5 7.67 *10^7 45.0
High 1 11780 1.37 * 10^10 2.5 7.67 * 10^7 178
High 2 11750 1.36 * 10^10 2.5 7.67 *10^7 178

JEOL 3200FSC

Procedure

  • Similar to Jeol 2100F, but use SA aperture 3 and Entrance aperture 3
Changed:
<
<

Tabulated Results

>
>

Tabulated Data

 
Aperture Area Avg counts Total Counts Current (pA/cm^2) Electrons Gain
EA 3 3.50 * 10^6 614.524 2.15 * 10^9 2.45 7.52 * 10^7 28.6
SA 3 3.48 * 10^6 614.294 2.14 * 10^9 2.40 7.36 * 10^7 29.1

  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

Revision 411 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
Changed:
<
<
  • Set beam intensity to 1 second exposre time at set magnification
>
>
  • Set beam intensity to 1 second exposure time
 
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
  • From CCD calibration, convert square nm to pixels, get dose in electrons/pixel
  • Gain = counts per pixel / electrons per pixel = counts per electron

Tabulated data

Magnification Dose (e/nm^2) nm/pixel Dose (e/pixel) Counts/pixel Gain
5800 7.298 1.308 39.4 1151.3 29.2
19000 199.2155   38.92 1169.99 30.06
25000 342.9676 0.352 42.5 1162.54 27.36
29000 448.6993   39.31 1134.07 28.85
50000 1418.9582 .170 41.0 1205.6 29.40
Changed:
<
<

Sublevel topic

subsub level topic

>
>

Jeol 2100F

Procedure

Added:
>
>
  • 50K Mag, spot 5, set intensity to 10 pA/cm^2 (small screen)
  • Set gain on CCD to desired level
  • Insert and center SA Aperture #3; beam should now fully fit on small screen
  • Read screen current on small screen in pA/cm^2
  • Take a 1 second Exposure image
  • Using ImageJ? software, box out area inside exposed circle and measure average counts, sd
  • Determine pixel area covered by SA aperture as follows:
    1. import image into spider
    2. Using th m command, threshold at level of (mean - 5 standard deviations)
    3. Using Hi T command, measure average of thresholded mask calculated above
    4. Pixel Area = 2048*2048*avg intensity
  • Total counts = Avg counts * pixel area
  • Convert current to electrons as follows:
    1. Diameter of small screen = 2.5 cm - > area = 4.91 cm^2
    2. 1 sec exposure means 1 Coulomb per Ampere
    3. 1 elecron = 1.60 * 10^-19 C
    4. Electrons = (pA/cm^2 * 4.91 cm^2 )/ (1.6*10^-7 e/pA)
  • Gain = total counts/total electrons

  • area of SA #3: 1.16 * 10^6 pixels

Tabulated Results

Trial Mean Counts Total Counts Current (pA/cm^2) Electrons Gain (counts/electron)
Low 1 2896.8 3.36 *10^9 2.5 7.67 * 10^7 43.8
Low 2 2902.2 3.37 * 10^9 2.5 7.67 * 10^7 43.9
Low 3 2984.3 3.46 * 10^ 9 2.5 7.67 * 10^7 45.1
Low 4 2977.1 3.45 * 10 ^9 2.5 7.67 *10^7 45.0
High 1 11780 1.37 * 10^10 2.5 7.67 * 10^7 178
High 2 11750 1.36 * 10^10 2.5 7.67 *10^7 178

JEOL 3200FSC

Procedure

  • Similar to Jeol 2100F, but use SA aperture 3 and Entrance aperture 3

Tabulated Results

Aperture Area Avg counts Total Counts Current (pA/cm^2) Electrons Gain
EA 3 3.50 * 10^6 614.524 2.15 * 10^9 2.45 7.52 * 10^7 28.6
SA 3 3.48 * 10^6 614.294 2.14 * 10^9 2.40 7.36 * 10^7 29.1
 
  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

Revision 311 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
  • Set beam intensity to 1 second exposre time at set magnification
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
  • From CCD calibration, convert square nm to pixels, get dose in electrons/pixel
  • Gain = counts per pixel / electrons per pixel = counts per electron
Changed:
<
<
  • Tabulated data
>
>

Tabulated data

 
Magnification Dose (e/nm^2) nm/pixel Dose (e/pixel) Counts/pixel Gain
5800 7.298 1.308 39.4 1151.3 29.2
19000 199.2155   38.92 1169.99 30.06
25000 342.9676 0.352 42.5 1162.54 27.36
29000 448.6993   39.31 1134.07 28.85
50000 1418.9582 .170 41.0 1205.6 29.40

Sublevel topic

subsub level topic

  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

Revision 211 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
  • Set beam intensity to 1 second exposre time at set magnification
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
Changed:
<
<
  • From CCD calibration, conve
>
>
  • From CCD calibration, convert square nm to pixels, get dose in electrons/pixel
Added:
>
>
  • Gain = counts per pixel / electrons per pixel = counts per electron
  • Tabulated data
Magnification Dose (e/nm^2) nm/pixel Dose (e/pixel) Counts/pixel Gain
5800 7.298 1.308 39.4 1151.3 29.2
19000 199.2155   38.92 1169.99 30.06
25000 342.9676 0.352 42.5 1162.54 27.36
29000 448.6993   39.31 1134.07 28.85
50000 1418.9582 .170 41.0 1205.6 29.40
 

Sublevel topic

subsub level topic

  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

Revision 111 Sep 2007 - Main.BillRice

 
META TOPICPARENT name="CemParameters"
Contents

Tecnai F20

Procedure

  • Go to low-dose Exposure mode
  • Set beam intensity to 1 second exposre time at set magnification
  • In SerialEM, set Record time to 1 second, with 1X binning
  • Take a Record picture and measure average intensity (counts/pixel)
  • In low-dose pullout tab, choose to measure intensity when screen is down and small screen is exposed (fully covered by beam)
  • This gives dose measured in electrons per square nm (ie mag taken into account)
  • From CCD calibration, conve

Sublevel topic

subsub level topic

  • Set ALLOWTOPICVIEW =

-- BillRice - 11 Sep 2007

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