Leginon

h1. Exposure Targeting Set-up for MSI-T for Four holes

[[New Exposure Targeting Set-up in MSI-T for Multiple holes]]

A good way to improve the throughput if there are multiple holes visible in a hl image is to target all four holes.

We can set up for 4 holes with this more challenging example:

h2. About this image:

This image shows the edge of the grid bar.  The intensity at edge of the grid bar has a mean around 20 while the rest has a mean around 45. The four holes are reasonably centered.

!original.png!

h2. Leginon/Exposure Targeting/Template>

* Cross correlation works better than phase correlation in this case because the hole does not have sharp edge and not perfectly round.

* Adjust the value to fill the mean before correlation to minimize the correlation along the edge of grid bar.

* Invert template for correlation if needed.

!template_corr_settings.png! !template_corr.png!

h2. Leginon/Exposure Targeting/Threshold>

* Fairly easy to set.

!threshold_settings.png! !threshold.png!

h2. Leginon/Exposure Targeting/Blobs>

* Allow more blobs than the intended 4.

* Use border to eliminate those too close to the edge.

!blobs_settings.png! !blobs.png!

h2. Leginon/Exposure Targeting/Lattice>

* Similar to that in Hole Targeting/Lattice step.

** Make measurement of the lattice distance

** Estimate the reference intensity for ice thickness filter.

!lattice_settings.png! !threshold_with_lattice_measurment.png! !lattice.png!

h2. Leginon/Exposure Targeting/Acquisition>

* Set up focus template but DO NOT eliminate focus targets using ice thickness criteria.  This works because Leginon (3.1 and above) will automatically choose the center most focus target.

* (3.5 and above) Activate "Apply ice thickness threshold on template-convolved acquisition targets" allows filtering of each convolution generated holes.

!acquisition_settings.png! !acquisition_all_focuses.png!