ISE-MeshTools Tutorials Tutorial 01 : working with

ISE-MeshTools Tutorials Tutorial 01 : working with
ISE-MeshTools Tutorials
Tutorial 01 : working with landmarks
Renaud LEBRUN1
1 Institut des Sciences de l’Evolution, Montpellier, France
Tutorial 01 includes:
•
One .vtk surface file representing a skull of Mus musculus
•
One .pos file
•
One .ori file
•
One .ver file
•
One .ntw file
•
The present .pdf document
Working with landmarks
Contents
1. About the specimen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2. Tutorial. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
2.1
2.2
2.3
2.4
2.5
Download and unzip files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2
A brief overview of enclosed files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Landmark digitization with ISE-MeshTools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Setting landmarks inside the mouse skull. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Saving landmarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
3. Acknowledgements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
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MeshTools Tutorial 01
1. About the specimen
The surface file enclosed in this tutorial represent three-dimensional reconstruction of the skull of a
house mouse (Mus musculus) obtained by computerized microtomography at the MRI µCT platform
housed at the ISE-M.
2. Tutorial
Before using this tutorial, please download and read ISE-MeshTools User Manual.
2.1 Download and unzip files
Download and unzip the files associated to this tutorial in a folder containing no accent. Open ISEMeshTools. Also, make sure that the path leading to the folder containing the tutorial files does not
contain any accent. Otherwise, ISE-MeshTools will not be able to open the contained files.
2.2 A brief overview of enclosed files
2.2.1 Mouse skull surface and position files
You may load the enclosed .vtk file (File -> Open Surface, then select “mouse_skull.vtk”). When loaded this way, the corresponding opened surface object is drawn grey, which indicates that this object
is selected. You may interact with selected objects in different ways (see ISE-MeshTools manual for
further explanations). As a general rule, when opening a new object, I strongly recommend to change
its position in order that it matches the 6 predefined camera positions :
When pressing “
“, object should be viewed from right side.
When pressing “
” object should be viewed from left side.
When pressing “
”, object should be viewed from front side.
When pressing “
”, object should be viewed from back side.
When pressing “
”, object should be viewed from above.
When pressing “ ”, object should be viewed from below.
Once correctly positioned, you may save the object’s current position (File->Position->Save Position).
The present tutorial contains a .pos file, which you may load in order to place correctly the house
mouse skull (File -> Open Position, then chose “Mouse_skull.pos “). If you plan to place landmarks
on internal structures, you may also select the skull object and change its transparency (Edit Selected
Surface->rendering modifications->Set Alpha Value -> then give a value smaller than 100).
You can unselect all opened objects by pressing “CTRL +D”, or select all objects by pressing “CTRL +A”.
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Working with landmarks
You can delete all selected objects by pressing “Del”.
2.2.2 Mouse skull project file
The present tutorial contains a project .ntw file, which may be useful to directly open the mouse
skull in a convenient position and to make it transparent. First, delete all currently opened objects
(press “CTRL+A”, then press “Del”). Then open the enclosed .ntw file (File->Open Project, then select
“Mouse_skull.ntw”). Once loaded, the mouse skull surface file object is opened, is given the position enclosed in the “Mouse_skull.pos” file, a colour and a transparency. Note that the newly opened
surface is unselected.
2.2.3 Mouse skull landmark file
Prerequisite : make sure that the mouse skull surface is loaded, and that it is correctly positioned. You
can load the enclosed .ver file (File->Landmarks->Load Landmarks-> Mouse_skull.ver), which contains
31 landmarks . You can change the way landmarks are rendered in the “General options” window
(Show->General options). You can chose to draw landmarks as spheres or as needles, and change
their display size in mm. In this tutorial, you may chose to display landmarks as needles and to set
their display size to 1.5 mm.
2.2.4 Mouse cranium .ori file
The present tutorial contains a .ori file, which contains orientation labels for the coordinate system
orientation helper. You can load this file the enclosed .ori file (File->Orientation labels, then select
“Mouse_cranium.ori”). Once loaded, the system coordinate orientation helper will show the following labels :
+z axis : dorsal
-z axis : ventral
+y axis : left
-y axis : right
+x axis : proximal
-x axis : distal
You may set your own orientation axis labels with the “Edit orientation labels” window (Viewing opt.> Orientation labels)
2.3 Landmark digitization with ISE-MeshTools
When setting landmarks, I recommend to press “ ” to activate the “Landmark mode”. When active,
only landmarks can be selected/unselected via right mouse button drag/click. Landmarks can be set
on surfaces by pressing “L” + left mouse click. If a single landmark is selected, its position can moved
on another part of the surface by pressing “L” + right mouse click (nothing happens if no landmark
is selected or if more than one landmark are selected). Also, you may need to move landmarks away
from the object’s surface (for instance when you want to place a landmark at the centre of a foramen): once selected, a landmark position can be moved by using the usual mouse (CTRL + middle
click + mouse drag) and GUI controls.
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MeshTools Tutorial 01
Two series of conventional landmarks can be set with ISE-MeshTools: “normal” and “target” landmarks. Press “ ” to activate normal landmark setting mode (this mode is active by default), “ ” to
activate target landmark setting mode mode.
You may need to reorder the landmark objects. Selected “normal”/”target” landmarks can be reordered using the following buttons. Pressing “ ” will place the selected landmarks earlier in the
“normal”/”target” landmark list, while pressing “ ” will place them one step further, respectively.
2.4 Setting landmarks inside the mouse skull
Depending on the “z” position of the camera, you may show/hide object, or object parts, which can
be useful to set landmarks inside inner structures. You may modify the “z” position of the camera
manually (Viewing opt. -> Camera -> Camera options: change “Tz” control) or interactively (move
the “cp” control = clipping plane slider laying centrally in the right panel of the main window). See
ISE-MeshTools User Manual for further explanations. Increasing Tz will tend to hide objects which lay
close to the camera (user’s point of view), and will tend to show distant objects. Decreasing Tz will
tend to show objects lying close to the camera (user’s point of view), and will tend to hide distant
objects.
For instance, a Tz value of 0 means that all the mouse skull parts situated before the origin
(x=0;y=0;z=0) are hidden, and that only the objects situated between the origin and “Camera far” are
displayed. In that case, it is now possible to set landmarks inside the endocranial cavity.
2.5 Saving landmarks
To save all digitized landmarks, go in “File->Landmark->Save Landmarks” or. “File->Landmark->Save
Target Landmarks”, depending on whether you want to save normal (red) landmarks or target (yellow) landmarks. ISE-MeshTools can manage two types of landmark files: “.LMK” “.VER” files. LMK files
contain a series of lines, each line being constructed the following way: landmark name (without
space or tab character), landmark coordinates. VER files contain a series of lines, each line being constructed the following way: landmark name (without space or tab character), landmark coordinates,
landmark orientation.
3. Acknowledgements
Thanks to the MRI imaging platform for the access to imaging facilities.
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