Leginon

h1. 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>

h2.  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.

h2.  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.

h2.  Original

h2.  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.

h2.  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.

h2.  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.

h2.  Display

To view the Edge image, enable this button. Enabling this button will

disable/override the Original, Template, and Threshold Displays.

h2.  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.

h2.  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.

h2.  Display

To view the Template image, enable this button. Enabling this button will

disable/override the Original, Edge, and Threshold Displays.

h2.  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.

h2.  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.

h2.  Display

To view the Threshold image, enable this button. Enabling this button will

disable/override the Original, Edge, and Template Displays.

h2.  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.

h2.  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.

h2.  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.

h2.  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..

h2.  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.

h2.  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.

h2.  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.