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Panel View Clip

Eugene Katrukha edited this page Mar 25, 2024 · 4 revisions

The panel under the view panel icon icon specifies volumetric dataset internal and rendering parameters:

View Clip panel

View

In this sub panel you can toggle:

  • show the origin of coordinates origin of coordinates icon, where each axis is colored according to the icon (X red, Y green, Z blue). Right-handed system is used.
  • render a box box volume icon around the original volume;
  • interface and render settings dialog settings button, described in detail below.

Render

Data

This selection box defines the way the dataset is rendered.
One can choose between "Max intensity" projection and "Volumetric" rendering.
"Volumetric" here corresponds to the "transparency rendering" or "alpha-blending" ray-casting.
Alternatively, one can switch between them using the shortcut O
Here is an example illustrating the difference of Maximum intensity vs Volumetric render:

max vs volumetric rendering

Each representation has its pros and cons, depending on the dataset.
Usually, the "volumetric" rendering can be tweaked to look better
using a separate opacity ("α range") slider in the Brightness and color (and opacity) dialog.

ROI Surface

This box defines a choice of ROI's rendering in the 'Surface' mode: "plain", "silhouette", "shaded" or "shiny".

ROI Surface

Voxel size

This subpanel specifies the dataset's voxel dimensions (anisotropy) and physical units.

voxel size change example

NB: Pay attention, all measurement results take these parameters into account.

Clipping

This subpanel allows dataset clipping by adjusting the range in each axis (in voxel units, not physical units).
The range can be moved by clicking and dragging the middle of the slider.

clip example

The clipping can be reset to the full volume using shortcut X.
"Show box?" checkbox adds an extra box around the clipped volume.
"Clip ROIs" checkbox will additionally clip rendered ROIs.
"Extract" button allows to extract clipped part as a new ImageJ window or save it to disk.

View Clip panel settings

This dialog under settings button button defines user-interaction and rendering settings

view clip settings

Snap area size on click (screen px) specifies an area where the maximum intensity voxel will be found upon clicking on the canvas. It is used in zoom/ROI point specification. The smaller area allows a more precise/narrow search of the voxel around the clicked location.

Transform animation duration (ms) refers to the smooth visual dataset transforms displayed on the canvas upon zoom-in, voxel change, etc. One can set it to zero to speed up the visualization.

Zoom settings

Clip volume when zooming in? will apply clipping equal to the zoom box size (see below) upon zoom in (shortcut D). See an example here.

Zoom box volume size (px): is the length of a cube box (in pixels) around the voxel with maximum intensity used to "focus" the view upon "zoom-in click".

Zoom box screen fraction (0-1): parameter defines how much of the canvas window width (or height, whatever is limiting) is going to be occupied by the final zoom box render at the end of zoom-in. This parameter also affects the final screen fraction of "zooming-in" on ROIs, when double clicked in the ROI list of Panel Tracing.

Perspective

Camera position and Near/far clipping plane positions. These parameters define how the perspective projection of the volume is built. You can read more about it at learnopengl, but here is an illustration of the idea:
perspective projection