Build Correlation Landscapes
Subtomogram alignment algorithms are usually implemented by maximizing the cross- correlation between the subtomograms and a template image. Instead of searching for the optimal parameter, we can calculate the correlation for all possible parameters and visualize the correlation as a n-dimensional heatmap. This heatmap is reminiscent of the "energy landscape" so we'll call it "correlation landscape".
Construct a Correlation Landscape
API: construct_landscape
GUI: Subtomogram Averaging > Landscape > Construct landscape
This method will calculate the correlation landscape around selected molecules.
List of parameters
- Set the template image and mask parameters in the STA widget.
- "layer" is the molecules layer that will be used to construct the landscape.
- "Max shifts (nm)" is the maximum allowed shift in (z, y, x) direction.
- "rotations" is the maximum allowed rotation angles in degree around each axis.
Two
float
values are expected for each axis.(a, b)
means the rotation angle will be between-a
anda
with stepb
. For example,(4, 2)
means the rotation angles will be-4
,-2
,0
,2
,4
. - "cutoff" is the relative cutoff frequency of the low-pass filter.
- "interpolation" is the interpolation method used for resampling the sub- volumes.
- "upsample factor" defines how many times the correlation landscape will be
upsampled.
5
means that the voxel size of the resulting landscape will be 1/5 of the original image.
Visualizing the Landscape
After the landscape construction, a Landscape
layer, a subclass of Surface
layer
will be added to the viewer. A Landscape
layer shows the surface of an arbitrary
threshold. You can adjust the threshold value in the layer control.