Preferred Leginon set up at the microscope
Added by Anchi Cheng over 12 years ago
This is a question from Steve Oneil.
In Leginon, a picture of an entire grid square is acquired at LM (~500x) and then all holes suitable for imaging are picked. If you use a 100-micron obj. aperture and 300-mesh grid, this is usually OK. But if you use a 70-micron obj. aperture and/or a 200-mesh or even a 100-mesh grid, then you will have a problem because of the following issues: 1. If the obj. aperture is not motorized, only part of a square can be seen in the LM image and some areas will be blocked by the obj. aperture. In this case you cannot pick all holes from one image. 2. If the obj. aperture is motorized so that it can be retracted automatically at LM, you have to use a much lower magnification to cover the entire square. In this case the image lacks details and may not be good for hole picking.
Can you tell us the preferred setting of your TEM (F20), i.e., the size of C2 and obj. apertures, the magnification and spotsize for all modes especially for the Exposure mode.
Replies (1)
RE: Preferred Leginon set up at the microscope - Added by Anchi Cheng over 12 years ago
First. see the section describing the criteria for sq preset.
The priority is to make sure that not too much of beam clipping by aperture is visible within the view of the CCD. Otherwise the correlation between images may have be too biased on the unmoved clipped beam. We normally do not lower magnification further to get the whole square if using 200 mesh grid, but rather pick multiple targeting on the same square.
The first set of values shown in the section Pre-MSI_set-up and the default Leginon settings shipped with the installation is our standard settings for up to 6-7 Angstrum resolution data collection. I added another example in the same section from a recent experiment. The experiment was aim for higher resolution and need to be combined with various changes in MSI-T settings in order to satisfy my criteria. Since the data are still being analyzed I'd better not to give full details in case we don't get higher resolution reconstruction : ).