Now I've gone
through some of
the different scan
methods you might use
to acquire 3D data
and the different
data types,
I want to talk
a little bit
about the process you would use
to create usable 3D
data for analyses.
So generally, as
I said before,
you're going to
want to mesh for
pretty much any analysis
you're going to do.
If you do a
surface scan,
this will generate
the mesh directly,
so all you'll be left to
do is clean the mesh.
However, if you
do a CT scan,
you'll need to take a
couple of extra steps
to create a mesh that's
usable for other analyses.
In these demos,
I will be using
a program called 3D
Slicer to do this.
The first step
would just be to
visualize the volume,
which you can do
by looking at
the different slice
views of the volume,
which will basically
just show you
different cuts
through the specimen.
And the other
thing you can do
is volume rendering,
as I showed in the
previous video,
to get an idea of
what the specimen
looks like as a whole.
Next, you want to crop to
your specific
specimen of interest,
since many CT
scans will contain
multiple pieces
because it's
more efficient to
scan that way.
As you can see
here, my scan of
the creodont Patriofelis
contains many
different elements
of that fossil.
But if I'm interested
in just the skull,
I want to crop
to the skull.
Finally, you'll
want to segment
the area or
the structures of interest
in order to
generate the mesh.
So in this picture
you can see everything
I've marked in
green is the skull,
which is the structure of
interest that I
want to create
a model of. The inside
part of the skull
that's grey
that's not marked
is the rock matrix,
which I don't want
included in this model.
And the outside black part
would be the air,
which I also don't
want to include in
this model. [3D] Slicer
isn't the only tool
available for CT
data processing
and in fact,
there are quite a
few other free and
open source tools
you could test out.
[3D] Slicer was
originally designed
for medical CT research,
so many of its tools
are designed
specifically for that.
However, it has become
much more broadly
applicable.
It can use
many different
data types and
many different
extensions have been
developed for it,
which gives it lots of
different functionality.
This is why I
prefer it over
the other options
I have listed.
The one downside
of [3D] Slicer is
that it requires a lot of
RAM or computer memory
in order to use correctly.
So if you don't have
access to a
powerful computer,
that's when you might want
to start looking to,
I would say either SPIERS,
which is paleontology
specific, or Drishti,
which is a more
general CT viewing
and processing application.
Paraviewer is
a very broad 3D
data viewing application
and processing.
And as far as
I've looked into it,
it seems like the learning
curve is quite steep.
>> So unless you have
much more complex
analyses going on,
I would not recommend
starting off
with it. Finally
ImageJ or FIJI,
which stands for
FIJI is just ImageJ
is not going to
generate meshes
from your volumes,
but it can be really
good for converting
formats.
So for instance,
you might want
to convert a stack of
images like bitmaps or
JPEGs into a single
NRRD or
even downsample your
images if you're using
[3D] Slicer and it's taking
up too much memory.
On the commercial side,
programs like Amira and
Avizo are definitely
going to be
more user-friendly
and maybe have
a bit more functionality
than this free software.
However, they are
extremely expensive,
which is why I do recommend
starting out on
the free software.
