Setup positions
Select points manually:
SerialEM:
- Navigator window, load grid square.
- Navigator window, Add points.
Select a grid of points (from SerialEM help file):
SerialEM:
Add Grid of Points command (Navigator – Montaging & Grids sub-menu)
Use this command to add a set of points on a regular rectangular
lattice. Four different kinds of grids can be defined: points in a
rectangle; points on a defined rectangular lattice to fill a polygon or
map; points along a line, and points at a defined spacing to fill a
polygon or map. For the first two kinds, the position of the lattice is
specified by a group of 5 points, three at corners of a rectangle and
two more adjacent to one of the corners. Here, holes that should be
marked with a point are shown with ‘X’ and the rest of the holes are
shown with ‘o’.
X o
o o o
o o
o o o
o o
o o o
o o
o o o
X o
o o o
X X
o o X
To make all of the points be in one group, press the ‘Add points’
button and mark all 5 points before pressing ‘Stop Adding’. As long as
one of the points is the current item, you can select this command. The
program will then ask for the label of a polygon that you want to fill.
If you leave the text box blank, it will create points for all
positions in the rectangle indicated by the corners. If you enter a
valid label for a polygon that contains the points (specifically, the
centroid of the points), then it will add points to fill the polygon,
extending the rectangle beyond the corners that you have marked if
necessary. If you are filling an elongated region, you can reduce
errors from extrapolation by marking the corner with two adjacent
points near the middle of the region instead of near one end.
Once you have added a grid with a 5-point pattern like this, you can
add a grid in a new area with the same spacing and orientation by
simply adding a single point in the new area. It must be the only
point in the group, so press ‘Add points’, add the point, and press
‘Stop Adding’. If you are not filling a polygon, the point should
be at the same corner of the region to fill as the corner of the
5-point pattern with two adjacent points. If you are filling a
polygon, put the point near the middle of the polygon to reduce
extrapolation errors.
To add a line of points, simply add a group of three points to indicate the extent and spacing of the line, such as:
X X o
o o o
o o X
As long as one of these points is the current item, the command will be
available and will add a line of points between the endpoints.
Finally, to add equally spaced points within a polygon or map but not
on a defined lattice, simply make the polygon or map be the current
item and select this command. Then enter the desired spacing in microns.
When adding points to fill a polygon or the rectangle of a map, the
points will not be placed right up against the border of the polygon.
Rather, a square box around each point is required to be fully within
the polygon. The size of this box as a fraction of the spacing between
points is controlled by the GridInPolygonBoxFraction property, whose
default value is 0.75.
Grid points can be added in two different patterns. One is a zigzag
pattern, which was the only pattern in SerialEM version 2.x, and was
designed to minimized stage movement when moving between points. The
other pattern goes in the same direction in each row and column, and
proceeds in an overall direction away from the location of the Focus
area in Low Dose mode. This pattern ensures that focusing is done in
areas that have already been acquired from. However, this pattern
is not used when added points are placed into separate groups.