Specimen Cooking Setup Dialog
This dialog box allows you to set the conditions for pre-exposing (cooking) a plastic section prior to a tilt series. If dose is calibrated for the selected conditions, then you can expose for a specified dose. Otherwise, you can simply set a time for the cooking. The general practice in Boulder to is to expose for about 2000 electrons per square Angstrom. Cooking with a well-spread beam should help to minimize warping of the section. Using the brightest spot for the cooking will reduce the time needed.
Setup mag and beam on scope
When this button is turned off, the dialog just shows the current parameter settings for the cooking. When the button is turned on, the microscope will be put into the specified state and the parameters can be adjusted simply by changing the magnification, spot size, and brightness on the scope.
Mag/Spot size/Intensity/Dose displays
The mag, spot size, and intensity readouts show the currently set parameters for cooking, and are dynamically updated when 'Setup mag and beam on scope' is turned on. The dose rate is derived from the spot size and intensity values, and will show '-x-' when dose is not calibrated for those values.
Expose for dose of
Select this radio button to cook until a specific dose is accumulated, and set the desired dose with the text box and spin buttons. Cooking will work with this selection only if dose is calibrated at the particular spot size and intensity being used.
Expose for time of
Select this radio button to cook for a specific amount of time, and set the desired time with the text box and spin buttons. You can always use this method of cooking, even when dose is not calibrated
Total time/dose readout
This line shows the total time when cooking until a dose is reached, or the total dose when cooking for a specified time. In either case, it will show '-x-' if dose is not calibrated.
Tilt to X degrees for cooking
Select this option to have the scope tilt to the angle specified in the text box for the duration of the cooking. Cooking at high tilt should be just as effective in terms of the dose rate, while exposing a wider area. However, it is essential that the specimen be close to eucentric before starting, so that the area cooked at high tilt will actually contain the desired area.
Note that if this option is not selected, the cooking will occur at whatever the tilt angle is when the cooking routine is started.
Restore specimen position after cooking
With this option selected, the program will take a reference picture at an appropriate magnification before starting, then take another picture at the end and align the two. Since shrinkage might make it hard to align these pictures, the program will search for a scaling of the second picture that maximizes the correlation between the two. It reports this scaling as a shrinkage value.
Use this button to close the dialog and start the cooking operation.