Biology Reference
In-Depth Information
lated. To edit a tick, simply double-click on the histogram
under the tick. A new tick can be added by double-clicking
where you want a new one. A color-editing dialog box will
appear. Remember than changing the transfer function doesn't
change the data, only how it is visualized. If at any point you
want to “apply” the current transfer function, you can use the
stack process “Apply Transfer Function” in the “Filters”
folder. This will change the data to match the transfer function
and reload a new transfer function.
7. How to choose the sigma of a Gaussian blur. The Gaussian
blur can be used for two purposes: (a) removing noise or (b)
removing “fl at” areas (i.e., contiguous area where all the vox-
els have close to the same value) and fi lling in gaps. (a) A
Gaussian function is signifi cant up to a distance of 2-3 times
sigma from its center. As such, to remove noise, a sigma about
the size of the noise is usually appropriate. (b) To fi ll gaps and
remove fl at areas, sigma should be about half of the size of the
largest gap or area.
8. The voxel editing tools can be used only on the work store. If
you just opened an image you can use the stack process “Copy
Main to Work Stack” in the “Multi-stack” folder. The voxel
editing tools work by replacing a cylinder in the volume by a
given value (by default: 0). However, only the parts visible on
the screen will be replaced, and the cylinder is always in the axis
of the camera (i.e., it is everything below the circle that
becomes visible by pressing the “Alt” key). Orient the view
and use the clipping planes to edit only what you need to
change and no more. There are three behaviors possible for the
editing tools: erase, fi ll, and seed. The mode depends on the
checkboxes “Fill” and “Seed” in the “View” tab. If none is
checked, the mode is “erase.” If only “Fill” is checked, the
behavior depends on the stack mode: if labelled, it will use the
current label; otherwise, it will use 65,535. At last, if both
“Fill” and “Seed” are checked, and if the stack is labelled, every
click will create a new label and use it to fi ll the selected area.
9. The stack process “Closing” in the “Morphology” folder
offers a more general algorithm to fi ll in (i.e., close) holes. It
will work for any shape but is slower and will tend to fuse
objects close to each other. The parameter of the process is the
size, in voxels, of the largest hole you want to fi ll in. It is worth
noting that if you use increasing values for the radius, the
result will be the same as if you had used directly the last value.
Therefore, the best strategy to optimize the value is to start
with small values, check with clipping planes that all the cells
are fi lled in, and increase the radius if needed. There is no need
to go back to the original image in the process.
Search WWH ::
Custom Search