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Camera sensitivity calibration with known dose rate

Added by Anchi Cheng over 14 years ago

In the manual part II and page 17.
The 6. and 7. Are following.
Sorry I do not quite sure I understand.
Posting for Yen-Chywan,

The Leginon/Presets Manager Preset Selector> Acquire does image. Then
Leginon/Presets Manager/Dose Image> Check the "dose" value. Then the manual
said "If desired dose is known, fill in the value and then click "match".
This will change the exposure time to give a close match of the value
entered." I do not sure I understand What exactly it means. Does that mean I
tell the program how many electron per angstrom square I want for this
preset and the program calculate how long of exposure time it should be base
on previous Dose calibration. If so, Since we did not really calibrate the
dose. And if I go to microscope and adjust the beam intensity and measure
the does by FEI control program, which make it close to 1000e/nm2s. Then I
go to leginon to Acquire does image. But if the Leginon/Presets Manager/Dose
Image> Check the "dose" value. And it is not 1000e/nm2 (off a lot for
example). How do I adjust it to close correct value?

Yen-Chywan


Replies (5)

Re: Camera sensitivity calibration with known dose rate - Added by Anchi Cheng over 14 years ago

Yen-Chywan,

Dose matching does require camera sensitivity (counts per electron per pixel area) calibration. This is done in Dose node in the Calibration application. Unfortunately, the node assumes a calibration using Faraday cup while most people do not have it. It is possible to enter the sensitivity value from camera manufacture, but that is not what you have. The number you have caught in the middle of the calibration.

Conceptually, here is what you need to do:

Definitions:

Dose rate: electron per specimen-area per second (you have this)

Camera sensitivity: image intensity (i.e. detector signal counts) per electron detected (This is what you want)

Camera Image Mean Counts: You need to take an unbinned, corrected CCD image at the dose rate you know to get this from the image stats.

Exposure time: the exposure time used to acquire the above image. in seconds

Effective camera pixel size at the magnification: What we called pixel-size at the given magnification as calibrated by Pixel Size node in the same application. It is the length a camera pixel covers at the specimen level (Make sure you have the number in the same length unit as used in Dose rate

Calculation:

Camera_sensitivity = Camera_Image_Mean_Counts / ( Dose_rate * (Effective_camera_pixel-size_at_the_magnification)^2 )

Once you enter that number in the Dose node ans save it, you can confirm it by matching dose again with known dose.

Anchi

Re: Camera sensitivity calibration with known dose rate - Added by Yen-Chywan Liaw over 14 years ago

Hi Anchi,

I will try to do that. But Gatan Taiwan Agent is suppose to come and measure the CCD sensitivity. But No one ever ask this before. So They are shipping the program from US to Taiwan. And will come some time hopefully.

Thanks

Yen-Chywan

Re: Camera sensitivity calibration with known dose rate - Added by Anchi Cheng over 14 years ago

"anchi" wrote:
Calculation:
Camera_sensitivity = Camera_Image_Mean_Counts / ( Dose_rate * (Effective_camera_pixel-size_at_the_magnification)^2 )

I missed the exposure time term in the formula. It should be:

Camera_sensitivity = Camera_Image_Mean_Counts / ( Exposure_time * Dose_rate * (Effective_camera_pixel-size_at_the_magnification)^2 )

RE: Camera sensitivity calibration with known dose rate - Added by Cheri Hampton over 14 years ago

I can't find where to enter the known camera sensitivity value, as per the manual: Leginon/Dose/Dose Settings/Camera Sensitivity> Enter Sensitivity values in counts per electron. This dialog box does not have Camera Sensitivity option

RE: Camera sensitivity calibration with known dose rate - Added by Jim Pulokas over 14 years ago

Sorry, we need to clean up the interface a bit, it is actually a dialog you get by clicking the green play button. To make it confusing, this dialog is also called "Dose Settings".

I am using this as an example to learn how to upload a screen shot into our wiki documentation. Now it should be more clear from the new screen shot:
http://emg.nysbc.org/projects/leginon/wiki/Dose_%28Camera_Sensitivity%29_Calibration
Also, modified the text on the wiki from "settings" to "calibrate". Still need to change the dialog title sometime.

Since you already know the value, enter in the box and click the "save" button, not the "calibrate" button.

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