Step To and Adjust IS Setup Dialog
This dialog opens when you press the Step To & Adjust IS... button in Multiple Record Setup dialog when in Low Dose mode and it allows you to specify which Low Dose area to take images with, what magnification to use, and whether to change the defocus offset if using View or Search. It is necessary to specify this in advance so that the initial image shift can be applied after going to conditions in which images will be taken. If parameters are set appropriately, there is an option to run the procedure automatically.
Low Dose area and images to use
Record (Preview images) is always available; View and Search are offered as options if they are not currently set to be in low magnification mode. As the name implies, with Record (Preview images), images will be taken with the Preview parameter set. A 2 x 2 Preview Montage is also always available, and a 2 x 3 Preview Montage option (or 3 x 2) is present to give an image closer to square when the current camera has an aspect ratio over 1.33 (e.g., a K3 camera). When one of these is selected, the program will open a temporary file for these montages and remove it at the end of the procedure. These montage options allow the adjustment to be done at a magnification closer to that of Record, where the image shifts are liable to be sufficiently close to the ones needed for Record.
Using anything but a higher magnification, near that of Record, has the same limitations and requirements as when initially setting the areas: images should be taken near focus unless there are good calibrations for the effects of high defocus. If there are image shift boundaries between the magnification to be used and the Record magnification (i.e., such that an applied image shift does not produce the same shift on the specimen at the two maginifications), then there need to be adequate calibrations of rotation angle and pixel size (i.e., 'RotationAndPixel' properties entries) to allow the image shift to be translated accurately from where it is measured to where it is used for acquisition.
Set Preview exposure to
Select this option and enter the desired exposure time for the Preview images. It will probably be necessary to have a longer exposure time when running the procedure automatically.
Magnification to use
The choices here are the Current mag of area, the Mag at which shifts were recorded, and a selected Other mag. When you have selected to acquire with the Record area, the latter two are liable to be successful if the magnification is a similarly high one; chosing a much lower magnification would have the same potential problems as using View or Search at such a magnification. If you have selected View or Search, using another magnification may impose a shift on the area unless the magnifications are well-aligned. Since all positions are going to be visited, such a shift is not an intrinsic problem, unless it prevents you from finding the first hole to be positioned at. There is an automatic change in intensity when switching to a different magnification, but it could result in the beam not being centered well enough.
Change defocus offset to
This option is available with View or Serach and allows you to switch from the currently set defocus offset to a smaller one if necessary. Like using a different magnification, changing the defocus offset may impose a shift that needs to be compensated for when positioning on the first hole.
Press OK to start the procedure; the program will go to the Low Dose area, with modifications if any, shift to the first position, and allow you to take images and store image shift values.
Any changes made to the chosen Low Dose area, either specified here or imposed by you after starting the procedure, will be restored when the procedure is finished.
Do procedure automatically with:
Check this option to run the sequence of operations automatically on a regular hole pattern after you press Start. In order for it be available, you must set the Hole size within 10% and select imaging conditions that will make the hole size be between 0.33 and 0.75 of the minimum dimension of the image (or between 0.17 and 0.75 for hex grids). The status line at the bottom of the group box will indicate why conditions are not met or how they are being met. When using single images, the program will crop the images down to a usable size if that contains enough pixels, or you can set the camera parameters to acquire a subset. No cropping is available with montages.
You can choose to have hole positions be adjusted either with Cross-correlation or with Hole centering. With Cross-correlation, the first image is used as a reference, so it does not matter whether the hole is off-center, as long as most of it is there and there is not much extraneous material. Images at the remainder of the holes are correlated with the first one. The cross-correlation can fail if the hole edge is not distinct enough, the size is not the same between holes, or if the correlation is thrown off by other contrasting material. At the end, single images are left in successive buffers with the last one in A and the reference in D, while montage overviews are in successive buffers with the last one in B.
With Hole centering, the program calls the Hole Finder with some parameters appropriate for finding one hole in an image with one or a few holes, and other parameters taken from pre-existing hole-finding parameters, namely as the geometry, spacing, filters, and thresholds. If the Hole Finder dialog is open when this dialog is opened, the hole size is taken from there; otherwise it is based on the last value used in this dialog. If there is hole at the center of the pattern (e.g., a 3x3 rectangular pattern or a hex array), the first image is taken at the center position and the hole is centered, with a relatively large image shift allowed. Images after that should be closer to center and require less shifting. At the end, all images are availlable for inspection is successive buffers, just as with cross-correlation. The method can give a poor result if montage pieces do not align well enough or if there is material intruding along one side that throws off the center measurement for a hole. Probably this method should be used only after finding cross-correlation inadequate.
With either method, the entry for Maximum shift as fraction of hole size determines whether a measured shift will be done; if a shift is too large, the procedure will be aborted.
Before starting, pick an area with relatively clean holes at the corners of the pattern to be assessed, which is determined by the current Multiple Record settings. When using Preview images or montages and starting with a View or Search image, be sure that the View or Search shift offset is well-calibrated (see Shift offsets for View and Search). Center on the central hole or center of the pattern and press Start.
Take image after shifting to position
Check this option to have an image taken automatically after shifting to each position, when not running the procedure automatically.
Close and Cancel
Close will close the dialog without running, but saving the parameters. Cancel will not save the parameters.