Leginon

Hideki,
The fact that you were able to move to even a wrong target means that
there was a calibration accessible to you.

I've looked at your database, it confirmed the above since the calibration you and I did were at the same magnification and instruments. However, the stage position calibration matrix were very different:
2x2 matrix:
Mine: 6.88132615391946e-08 | -3.22671833452268e-09

-2.72846792177793e-09 | -7.58786291851175e-08

Yours: 7.07759017200733e-08 | -3.81132827361493e-09

2.85140573173201e-09 | 7.56808290025043e-08

This tells me that your camera is flipped in the second axis relative to mine.

This is something we didn't check that day on T12. My calibration makes it move the opposite direction from yours. Since you log in as a different user from what we did last week, your Digital Micrograph (DM) Camera Configuration is different. Here is the whole list of what it should be as a standard at NRAMM. You may establish your rule at your site about the camera flipping, and the shutter part need to match your physical wiring.

First, find out which camera control digital output is connected physically to the pre-specimen shutter on the microscope. This should be the shutter used for low-dose imaging. You will need to find it out from your microscope engineer or those who install the camera. In most cases we've seen, this is shutter 1, also known as primary shutter in DM. The next part use this as the example.

Second, start DM from the Menu bar, go to /Camera/Configure Camera...
This brings up the Camera Configuration Window.
1. Set Shutter 1 to what is connected physically to your camera control box. In this examples, pre-specimen shutter. Set Shutter 2 to the other one (post-specimen in this example).
2. Choose the Idle Shutter State. For low-dose mode, only pre-specimen shutter is used. Therefore, in this example, you would set Shutter 1 to closed and leave Shutter 2 to open.
3. Choose to flip the camera axis if desired. Our standard at NRAMM makes the image acquired and displayed in DM or Leginon to have the same orientation as what is viewed as one sit at the microscope. You can check it by acquiring an object of known orientation such as an offsetted pointer device. At NRAMM, this happens to require a flip.

Third. now that the exposure will need to be made by opening the pre-specimen shutter, you should change these at your three recordning modes built in at DM. This is under the menu /Camera/Camera Setup
For each of the mode (Search/Focus/Exposure), since in this example shutter 1 (primary) is the pre-specimen
shutter that is normally closed, you should uncheck the box on "Use Alternate Shutter".

To check that your shuttering is right, you need to look at the LED on the camera control box. While the microscope main screen is down, LED lights for the two shutters should be on, meaning the shutters are open. When the main screen is up and the camera is inserted, the shutters would go to idle state, with the one correspond to the pre-specimen dimmed while the one for the post-specimen lit. Next, try to acquire an image through leginon at a relative long exposure ( > 0.5 s), and watch the LEDs. The one for pre-specimen should light up during the time of the exposure and then become dim again.

Camera flipping and shutter settings are configured per computer user. If you have several users, you will need to sync the flipping practices and make sure all of you are shuttering correctly.

Anchi

Anchi,

Thanks for the information.
I've got back to the original state you set it up last time. The problem we had is a kind of an easy mistake but sometimes may happen to us.

Thanks

Hideki