hello this is Remy from the 3d
applications team by following this
tutorial you will learn how to
interactively create a segmentation of a
3d image please note that this tutorial
provides only an example of usage of the
segmentation editor using only the
features from the basic software package
more advanced features or usages of the
segmentation editor are presented in
other video tutorials or in the user's
guide a segmentation assigns a label to
each pixel of the image which describes
a region or material associated with a
pixel the segmentation is taught in a
separate data object called a labeled
field the segmentation is a prerequisite
for surface model generation or accurate
quantification such as volume
measurement depending on the situation
pre-processing or image the noising
should be performed before segmentation
the process of segmentation itself can
be automatic or interactive depending on
the input images and desired results the
segmentation editor is workrooms that
provides a dedicated user interface for
interactive segmentation tasks will work
on the file chocolate bar which can be
loaded from the folder data
tutorials right click on the green icon
and select edit new label field from the
image segmentation section this will
automatically launch the segmentation
work room setup by replacing the user
interface at the same time and not
currently visible new data object will
be added to the project view which also
segmentation results
the segmentation editor operates by
default in for viewers mode in this mode
free slice viewer with X Y or Z
orientations are shown together with 3d
viewer alternatively single or to the
world layouts are possible you can
change the orientation of a 2d viewer by
either selecting another orientation
from the segmentation orientation menu
or by clicking on the orientation
presets in the viewer toolbar
in the slightest viewers you can use the
slider at the bottom to scroll through
the slices or roll the mouse wheel you
can also address the zoom for each slice
you were independently directly in the
upper right corner of the corresponding
of your well for all viewers you may
address the quorum app using the display
control tools
the general principle of the
segmentation dito is to first use
selection tools to select some pixels
optionally modify that selection using
the grow or shrink buttons or the
selection menu and finally assign that
selection to a material for instance the
paint tool allows to select pixels
directly by painting them onto 2d slices
selected pixels are shown with a red
overlay in the slides you will and also
in red in the 3d viewer the assignment
to a material is done by selecting the
material and pressing the plus button
let just clear the selection for the
moment and see how we can segment a data
set
this tutorial present one approach to
segments is chocolate bar into four
phases to bar itself composed of a
chocolate coating a layer of caramel and
the most feeling as well as air bubbles
let's start with a simple threshold
select the threshold tool from the
selection area of the segmentation
editors main panel adjust the masking
range such that the blue mask includes a
whole chocolate
once a reasonable masking wrench is
selected let then press select mask
voxel to perform the selection then
select a target material and add the
selection to that material you may
rename the material change its color or
appearance in the 2d viewers at any time
by right-clicking on the material name
it appears at the chocolate bar contains
many large air bubbles which will not
capture by the threshold operation in
order to capture them and assign them to
a new material let's first create that
place order and name the material
bubbles
in order to select the bubbles a simple
procedure can be to reselect the whole
Bell and then modify the selection to
fill old in free using the menu if we
know lock the material inside and assign
the selection containing the bar and
it's old into the bubbles material then
only the bubbles get assigned to the new
material as can be expected the lock
option prevents voxels belonging to a
material from being related don't forget
to unlock the material once you no
longer need them locked please note that
the segmentation little offers the
option to undo the recent action in case
mistake was made
at this date using the menu segmentation
material statistics we can already
compute the volume of the chocolate bar
and the amount of air inside it as well
as a few other basic measurements more
advanced measurements are available in
other parts of the software and
discussed in other tutorial let's
continue with the segmentation and
segments a mousse filling visible as a
dark ray in the image in a new material
for this we will use a magic wand tool
this tool basically grows a selection
starting from the clicked pixel and
propagating into address and pixels
provided the respect look requested
intensity range
a useful trick here to address the
threshold value is to position the mouse
cursor on the box and rotate the mouse
wheel to address the value and update
the display simultaneously as the
original image is fairly noisy the
obtained selection contains lots of
holes and irregularities in order to
smooth them out we will grow the
selection three times
fill holes and shrink the selection back
if onlys morphing is intended you should
grow and shrink the same number of times
now let's lock the bubbles material and
assign the selection to the most
material
in order to segment the caramel layer
since the difference of gray levels with
the chocolate is very low and the noise
is quite strong we will rely on manual
segmentation and use shape interpolation
to accelerate this manual process
let's start with one end of the lair for
example see slice 286 and use the paint
tool to select the caramel layer on that
slice using ctrl + left click you can
erase from the selection and with a
right-click you can fill in the selected
areas that is enclosed by your selection
now let's move to an slice further away
for example slice 200 and select the
caramel on that second layer
now we can use the menu selection
interpolate to interpret a selection
between those two slices please note
that this interpolation operates only on
the shape of the selection and does not
take any critical information into
account we may use any selection tool
for this interpolation process as long
as we use only two the selection and
always in the same 2d view for example
and continue with the lasso tool in
autotrace mode to process slice 100 and
maybe the last slice as long as only
through the barrel selections are being
made so interpolation will fill in the
gaps between consecutive plates
now let's lock the bubbles and the most
materials and assign that selection to a
new material caramel to finish with the
segmentation let's lock only the bubble
material and use smooth 3d to smooth out
a label field while preserving the
bubble
of course different types of him
may require different strategies for
performing the segmentation efficiently
more advanced interactive segmentation
techniques are also presented in other
tutorials at this stage so user can now
come back to the project workroom for
example to visualize a segmentation data
or to carry on with quantification or
survey generation these possibilities
are also covered in other tutorials
the present tutorial introduced you with
the main principles and tools of the
segmentation editor and how to use them
to perform interactive image
segmentation thank you for following it
goodbye
you