Work with Cameras on F20

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Gwenda Allen
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1 Chen Xu $BrandeisEM: ~emdoc/en_us.iso8859-1/articles/work-with-cameras-on-f20/article.sgml,v0.1, Tue Nov 20 11:55:47 EST 2012 xuchen Exp$ Currently, there are three cameras on our F20 scope. They are FEI Falcon camera, Gatan Orius CCD camera and Gatan US4000 CCD camera. Falcon is a direct electron detector. Orius is a setup camera equipped with Falcon as part of the system. US4000 is transferred from F30 on which a new Gatan K2 camera system is installed. The FEI Eagle CCD camera was dismounted and returned to FEI. Due to the special properties of the new Falcon direct electron detector, some new features of Tecnai software are intruduced in the newly updated Tecnai version beta. These teatures are mainly to protect Falcon camera sensor from over-dose irradiation. The external shutter control for various cameras is also changed from old style to a new integrated fashion. Some harward change is also invloved accordingly. In this document, I try to provide all basic information about all three cameras on the F20, both hardware and software wise. You can also get pdf version of this document here (article.pdf). Table of Contents 1. Some Properties of the Three Cameras Camera Physical Mounts and Controllers Mag & PixelSize (at specimen level) Calibration table About Dose Protector About Shutter Control with All Three Cameras A Normal Starting Up Procedure for Daily Operation Some Properties of the Three Cameras FEI Falcon Dierect Electron Detector: Physical pixelsize at chip is 14um. The viewsize is 4k X 4k. 1

2 This is a 1st generation chip, not back-thinned. This is a CMOS type, 16-bit camera. Bottom mount, retractable by motor driven, but NOT from SerialEM. The conversion efficiency (counts per primary electron) are: 190 for 200kV and 313 for 120kV. Gatan Orius SC200 CCD camera, Model 830 2k x 2k CCD sensor Progressive interline device (2048 x 2048 pixels, 7.4um each) 14 bit dynamic range Conversion Efficiency: ~12 counts/primary electron (120kV) Frame rate: 4x binning On-axis bottom mount, retractable Gatan US4000 CCD camera area = 4k x 4k, with a P type scintillator facing electron pixelsize on chip = 15um 4-port readout Conversion efficiency: ~ 14 counts/primary electron at 300kV, ~22 at 200kV and at 120kV. Dynamic range: 16 bit Bottom mount, retractable 2. Camera Physical Mounts and Controllers Here is a picture showing how three cameras are mounted on-axis after viewing chamber. 2

3 FEI Falcon direct detctor and Gatan Orius are mounted in head-to-head configuration. And US4000 is mounted right below the housing piece for Falcon and Orius. Therefore, all three cameras are on-axis and retractable. Below is a picture showing all camera controllers and an FEI central shutter unit (CSU). 3

The CSU is a centralized controller starting to appears with Titan. All the shutter signals from each cameras controller are input to this unit and the unit sends out shutter signals to microscope.

4 The CSU is a centralized controller starting to appears with Titan. All the shutter signals from each cameras controller are input to this unit and the unit sends out shutter signals to microscope. TIA has to be started up before this shutter control unit works properly. 3. Mag & PixelSize (at specimen level) Calibration table The calibration was done using standard 0.463um distance grating grid and <001> oriented Au crystalline standard specimen. It is obtained using an FEI software "MagCal". It measures pixelsizes at each and all the magnifications for one camera and interplates values for rest two cameras. These calibrated values are believed to be accurate enough for SerialEM automation and normal usage. If you have concern about the accuracy for one specific magnification for high resolution sturcture purpose, it is recommended to double check it using special standard specimen such as TMV or Tropomyosin Para-crytals. The mag and pixelsize information in the table here is mainly for reference purpose. The images taken by either Tecnai/TIA, Gatan DiditalMicrograph(DM) and SerialEM have this info embedded in the images already. Index_Mag Mag_ScreenDown(X)Mag_ScreenUp(X) Pixelsize(nm) - Orius(7.4um, 2kX2k) US4000(15um, 4kX4k)

5 Index_Mag Mag_ScreenDown(X)Mag_ScreenUp(X) Pixelsize(nm) - Orius(7.4um, 2kX2k) Work with Cameras on F20 US4000(15um, 4kX4k)

6 4. About Dose Protector Work with Cameras on F20 In order to prevent Falcon ship from over-dose irradiation, Tecnai intrudoces a new software component called "Dose Protector". Everytime when you start up TUI interface, you will have to calibrate a dose intensity before you can use Falcon camera. Otherwise, the beam gets planked as long as Falcon camera is in inserted position. Calibrating the dose intensity is very simple, you follow a three-step instruction from screen and then you are done. As hinted above, if you don t plan to use the Falcon camera for your session, you can skip it. The protection from Dose Protector is very rubust. It acts at TEMserver level. For example, before you calibrate the dose intensity or your beam intensity is out of the calibration range, you can not get an image from Falcon camera. If you do insert Falcon camera and try to take an image using SerialEM, you will get an error message rather than getting a blanked image. This is very good, as we won t need to worry about possible damage from using the third party software - SerialEM! 5. About Shutter Control with All Three Cameras In the past, Gatan camera controls shutter by directly sending 5V signal to gun tilt coil or/and projector lens coil. This is no longer the case anymore. Instead, all the shutter cables from camera controllers go to Central Shutter Unit (CSU) to which FEI Tecnai has total control. It might not sound anything troublesome. However, it results in a freedom loss at selecting camera via non-fei software interface. For example, you can still select different camera from Gatan DM interface, but imaging from Gatan intreface won t have proper control to shutter. You can get an image, but the image is not right. The same thing happens to SerialEM, you can get image, but the image might not be good. The only way to get shutter control correct is to also select the same camera from FEI -> TUI -> Camera -> camera list. This makes freely switching camera in scripting (macro) command impossible. 6. A Normal Starting Up Procedure for Daily Operation Log into F20 Tecnai computer. Start interfaces IN ORDER: TUI, DM, TIA. Select "Falcon" from camera list in TUI, then Start up SerialEM. 6

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