Hole Depth¶

The hole depth node, is a set of tools to measure parameters needed to correlate the
intensity values of hole with (I) and without ice (I0) with the physical thickness of the ice.
The two intensity values gives the image contrast , c=ln(I0/I), that is used in Hole Finder
Node Class as the relative measurement of thickness. Since the actual calibration of contrast
against physical thickness is not yet written, we do not advise using this node unless you
plan to perform your own query and fit the values with the proper function outside
Leginon.

Required bindings for recieving images:

<highlights>
<simplelist type="vert">
<member> This node at the moment stands alone and is used in post session
processing.</member>
</simplelist>
</highlights>

Image Selection¶

Each selected image type are for different measurement required for the correlation.

• I0= Image of the area after the ice is burned recorded at the magnification and
  defocus at which the contrast-thickness calibration is intended.

Relevent Image Control Panel-

• PickHoles: Pick location and calculates mean intensity within given radius of
  the the Picked position.

• I= Image of the area before the ice is burned recorded at the magnification and
  defocus at which the contrast-thickness calibration is intended.

Relevent Image Control Panel-

• PickHoles: Pick location and calculates mean intensity within given radius of
  the the Picked position.

• Hole Untilt= Image of the a small patch of ice burned away from carbob support at
  high magnification that is used to determine the radius of the burned cylindrical
  hole.

Relevent Image Control Panel-

• Original: File Entry.

• Edge: Create Edge Image of the hole.

• Template: Create Ring Template and correlate with the edge image to obtain
  the radius of the cylindrical hole.

• Hole Tilt= Image of the same area as "Hole Untilt" with the stage tilted to
  reveal some separation of the two cylinder end projection or partial ocluded path by
  one of the end projection.

Relevent Image Control Panel-

• Original: File Entry.

• Edge: Create Edge Image of the tilted hole.

• Template: Using the tilt-projected ring template created from "Hole Untilt"
  and the microscopic stage alpha angle of the tilted image to correlate with the
  edge image to obtain the correlation peaks of the the two end of the
  cylinder.

• Threshold: Threshold the correlation image to reveal only the two main
  peaks.

• Blobs: Find the two thresholded peaks and calculates the depth of the hole
  from the separation.

Image Control Panel¶

NOTE: To see the effects of Testing the settings for a particular Hole Depth step in
the Image Control Panel, the corresponding Hole Depth step Display must be enabled before
using the Test feature in that step's Display Settings.

Original¶

Display¶

To view the original input image without any image processing done to it, enable
this button. Enabling this button will disable/override the Edge, Template, and
Threshold Displays.

Display Settings¶

• Original Image: File Entry = Enter the path and name of an MRC image that
  matches the Image selection chosen in the node toolbar. The filename and path for
  each type are stored separately. Only the chosen type will be displayed.

Edge¶

The purpose of the Edge step is to convert the original image into an "edge" image
where the edges of the holes in the image are enhanced against a black background.

Display¶

To view the Edge image, enable this button. Enabling this button will
disable/override the Original, Template, and Threshold Displays.

Display Settings¶

• Low Pass Filter Sigma = Enter the sigma of the low pass filter applied to the
  edge image. A value of 0 will not apply a low pass filter to the edge
  image.

• Edge Finding Threshold = Enter a reasonable intensity value that will enhance
  the edges of the hole(s) in the edge image.

• Test = Press this button to test/apply the LP sigma and Edge Finding
  Threshold effects on the edge image.

Template¶

The purpose of the Template step is to cross correlate a template of the properly
sized holes against the edge image where the edges of the holes have been enhanced in the
previous step. Unlike in HoleFinder, this template is a tilt projection of the circular
ring.

Display¶

To view the Template image, enable this button. Enabling this button will
disable/override the Original, Edge, and Threshold Displays.

Display Settings¶

• Use "phase | cross" correlation = to do this calculation.

• Rings (Add|Edit|Delete) = Add|Edit|Delete the inner and outer hole (ring)
  diameters in this section. Use the ruler tool while displaying the Edge image to
  measure the average inner and outer hole diameter. Enter the average inner and
  outer hole diameter in this section.

• Low Pass Filter Sigma (for Phase Correlation only) = Enter a low pass filter
  sigma that is used only when phase correlation is used in this step.

• Tilt Axis = Enter the angle in degree the tilt axis is measured from the
  y-axis of the image. Positive is counterclockwise.

• Test = Press this button to test/apply the parameters that have been adjusted
  in this step.

Threshold¶

The purpose of the Threshold step is to apply a threshold to the previous Template
image. It is in unit of correlation. The Threshold image should have dots that represent
the center of all the found holes.

Display¶

To view the Threshold image, enable this button. Enabling this button will
disable/override the Original, Edge, and Template Displays.

Display Settings¶

• Threshold = Enter the Threshold value of a dot that represents the center of
  a hole (relative to the value with the stdv shown for the correlation
  image).

• Test = Press this button to test/apply the Threshold to the template
  correlation image. Only the dots hat represent the center of the holes should
  appear. It is highly likely that dots not representing the center of a hole will
  also appear.

Blobs¶

The purpose of the Blobs step in Hold Depth is not only to mark the center of the
thresholded image but also to calculate the depth of the hole from the two marked
locations.

Display¶

To view Blobs, either the Original, Edge, Template, or Threshold Displays must be
enabled. The Blobs that pass this step or manually picked will be shown with a turquoise
crosshair.

Display Settings¶

• Border = The pixel value distance from the edge of the image where all
  potential hole targets will be erased.

• Max. blobs = The maximum number of hole targets or blobs at this point that
  are allowed. If the number of blobs exceeds this number, the extra blobs will be
  eliminated.

• Max. blob size = The maximum size of a blob that is allowed to pass. This is
  roughly the square of an average blob diameter. Use the ruler tool on the
  Threshold image to determine the average diameter of a blob.

• Find blobs / Calc depth= Press this button to test/apply the Blobs criteria
  to the Threshold image and calculate the depth of the hole if 2 blobs are found.
  If only 1 blob is found, the correlation peaks are considered unresolved and a
  separation of 1 pixel is assumed in the depth calculation.

• Calc w/ selections= Press this button to calculate the depth of the hole
  using the two manually picked blobs..

Pick Holes¶

The purpose of the step is to locate the burned position in either the images before
or after the burning and to calculate the mean intensity within given radius.

Display¶

To pick and calculate mean intensity of the Picked Holes, the Original Displays
must be enabled. The acquisition targets that pass this step will be shown with a green
crosshair.

Display Settings¶

• Hole Statistics Radius = The radius in pixels of the holes (that pass the
  lattice criteria) that will be used to determine each hole's statistics.

• Hole Statistics Zero Thickness = The intensity value of an empty hole, i.e.
  zero thickness intensity.

• Shiftpicks = If a hole has been picked and tested from I0 image, pressing this
  button with a I image loaded causes the current picks shift by the offset of
  correlation peaks between I0 to I.

• Test = Press this button to test/apply the zero thickness and radius criteria
  to calculate the mean intensity of the picked hole.

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