Leginon

These are two different errors. I think you will get the first error, too, with CCD if you clear the error line in the logger with "delete" button on the keyboard.

Error 1 says no reference target in "Dose Measurement" node. See Running MSI-Tomography application in the section for Dose Measurement. However, if your scope beam intensity is stable, you can ignore this error and do without dose measurement.

Erro 2 is about movement error. This is actually normal. To achieve accurate targeting by not so perfect goniometer, Leginon move multiple time with Navigation node in tomography application. You should see the wheel of that node spinning before seeing this error in Tomography node. As a user, you decide what is consider acceptable error in the Settings of Tomography node. See MSI-Tomography_Preferences and Ways_of_Moving_to_Targets_in_Nodes_that_acquire_images_inside_MSI for more explanation. You can increase "Navigator Acceptable Tolerance" in Tomography Settings if you think a larger error is still good enough to include the object you want to do tomography on in the tilt series. Any Tecnai/Polara goniometer should be able to use multiple movement method to take you within 0.1 um 90 % of the time. Post a screenshot of the navigation node showing the logger and image/correlation map if this continues to happen.

Neither of the screenshot is related to the pixelsize calibration error. Could you get me one of that? Seeing where it came from helps me determining the source.

p.s. We have not collected tilt series with DD yet. Leginon tomography fine-tunes the exposure time to give even dose at different tilts. DE-12 can only change value by 25 ms (one frame at 40 frames per second). It means that you have to use a very weak beam and long exposure to allow this to function. Otherwise you will need to accept images with very different intensity in the same tilt series and a large uncertainty on how much total dose the specimen receive.

One more point, the movement is done with the parent image (the image where you picked the target for tomography). If it is complaining about pixel size error, it would for that preset, not the one you use for collecting the tilt series.

Anchi

Hi Anchi, you were right: I had the wrong magnification for sq. After changing this to the one I had done the calibration for, the target moving worked. However, when using the exact same presets, but now collecting on the DE12 in tomo, that error about the pixelsize came up again. It doesn't complain about this in the CCD with the exact same mag though! (And the values are entered in the pixelsize calibration table). I attached a screenshot of this error.

Mandy

Btw... navigation at 15500x (mag for tomo) works fine (see screenshot). Navigation is done on CCD, if pixelsize was not known it wouldn't be able to do this either, right?

Ver confusing indeed. Can I come over now? Reply by e-mail please.

After an on-site trouble shooting, here is what happened for future reference.

In their setup, there are both CCD on the scope-controlling computer and DE camera located on a separate computer. All Leginon applications should have use the ones with postfix of 2. See Using_Leginon_on_a_system_where_the_microscope_and_camera_are_controlled_by_different_computers

1. The pixel size and other calibrations for DE-12 were done with the application "Calibrations" not "Calibrations2" by mistake. All calibration nodes also used "overwrite preset" option that were set to Gatan Camera on the scope-controlling computer. Therefore, none of the calibrations they thought belonging to DE-12 were not recorded as such.
2. Applications such as MSI-T2 was used correctly. Since DE-12 was used only in the final exposure. It did not cause calibration error since all movement were done with the CCD controlled by the scope computer.
3. MSI-Tomography2 was used correctly. However, in this case, Tomography node requires pixel, image shift, and stage calibration of the "tomo" preset from DE-12. The pixel size is for conversion of the goniometer model from physical unit to pixels. The image shift is for tracking the feature by image shift. The stage calibration is for determine how to stretch the tilted images to give the same scale as the untilted on that improves the correlation between images of different tilts.