In this document we provide a brief introduction to the concepts involved with the sectionView and MAPaint software. It is recommended that if you have not used the software before then you should at least read the Introduction below.  You can then go directly to the Quick Start -further details section for a minimal set of instruction for getting the program running and displaying arbitrary sections and anatomy. If you want to know more details of the system and its underlying design assumptions please read the technical documents available from our web site although beware that the user-manual is not yet complete and may have some parts that are now out of date. Finally the System Requirements section details the systems that can be currently used to run the program.

• Introduction
• Installation
• Quick Start - further details
• MAPaint Mini-Manual (on this CD)
• MAPaint User-Manual (from our web site)
• MAPaint Program and Geometry Paper (from our web site)
• System Requirements

Introduction

The core concepts in sectionView are:

• there is a 3-D grey-level voxel image, termed the reference image or reference object;
• there are regions of space (arbitrary sets of voxels) within the 3D reference image volume, which are associated with a particular label.

As the name implies, sectionView is a program that allows the user to view sections through the digital embryo. The sections can be at any orientation and position through the block and is not constrained by the original sectioning planes.  Once a section orientation has been defined the program provides a simple slider control to allow the user to pan through the volume displaying successive parallel planes, simulating a physical re-sectioning of the embryo. The program allows any number of section view through the same volume which are displayed simultaneously.  To provide some idea of the relative 3D orientations and positions the program interface includes a 3D view of the volume with outlines of the currently displayed sections. This navigator window provides useful feedback but only displays boundaries. For more realistic surface and volume rendering in 3D, other programs are required.

Once a reference image has been selected and read in, any domains that have been defined within that image can also be read in and will appear as a coloured region within any section. Optionally the domain outline can be displayed in 3D in the navigator window. Up to 32 domains can be read in simultaneously (10 by default). When a domain is read in it will be added to (form the set union of) any voxels already assigned to the selected colour.Therefore it is possible to generate combined domains from multiple inputs. If you are using MAPaint each section view window can also be used to modify the extent of the domain within that window. When confirmed, the modification will immediately propogate to all other views.

When used in conjunction with the CD-ROM, sectionView can read in the anatomy data associated with a particular Theiler stage and allow the user to display the anatomical domains and to query what anatomical component is associated with any particular voxel. The program will give interactive feedback of the anatomy underneath the cursor.

For more details on the operation of sectionView and MAPaint please read the mini-manual available on this CD and the technical document available from the genex web site.

Quick Start  -  further details.

Starting sectionView/MAPaint without installation:

• With the CD-ROM inserted find the CD-ROM directory (<CD-ROM path>). On a Sun machine <CD-ROM path> is probably "/cdrom/cdrom0".
• Determine your machine type (<MACH>):
• Sun workstation SunOS 5.6 (Solaris 2.6) or newer, not elite graphics: <MACH> is s2
• Sun workstation SunOS 5.6 (Solaris 2.6) or newer,  elite graphics: <MACH> is s2_elite
• Sun Workstation SunOS 5.5 (Solaris 2.5, 2.5.1): <MACH> is s2_elite
• SGI, IRIX 5.3+: <MACH> is sg (to be included soon - query ma-tech for details)
• In a terminal window (i.e. with a command line) start up the program (substituting appropriate values for the cdrom directory and machine type):
• <CD-ROM path>/macd/bin/<MACH>/MAPaint -cdrom <CD-ROM path>/macd/reconstructions &


Note MAPaint and SectionView will only work if you have set your browser application preferences for the Woolz MIME type to be MAPaint (see setting preferences to using SectionView and MAPaint from the CDROM ).

Displaying and manipulating an orthogonal section view:

• Start sectionView/MAPaint (e.g. click "sectionView" on the Theiler 14 page,  or start the MAPaint program in an xterm window). The top-level window with menus and navigator view should appear.
• If you didn't start from the Theiler 14 page: from the "File" menu select "ts14" from the "Theiler Stage" menu entry wait for the image volume bounding box and embryo outline to appear and for the "Anatomy" menu button to become solid (not greyed out).
• From the "View" menu select "X-Y view..." and move the resulting dialog popup away from the navigator window. At this point the bounding rectangle of the view will show in the navigator window as a yellow rectangle.
• Move the cursor over the section image - the section bounding rectagle should turn red.
• Click and drag the "Distance" slider left/right - the section image will change and the bounding rectangle in the navigator window should move up and down.
• Try the controls in and on the "Section" frame of the view window: toggles "filled 3D view" and "view direction";  buttons "mag+" and "mag-" - note scroll bars should appear on the view window.
• Set the distance slider by typing in a new value.
• Select another orthogonal view from the "View" menu e.g. "Z-X view..." - you may need to resize the window to see the whole view without scrolling.
• Two bounding frames should now be visible in the navigator window and the intersection of one frame with the other should be marked by a green line in each view.
• Adjust the "Distance" slider in one view to see the green line move into the other.
• Move the cursor from one view to the other  - the red bounding rectangle should change in the navigator window.

Adjusting the Navigator View

• Click the left-mouse button over the 3D view in the middle of the navigator window, drag left/right and up/down - the view will change as if rolling a globe view of the object.
• Release the left mouse button with the cursor still moving - the view should continue to rotate.
• Stop the rotation by clicking again on the display and hold in the cursor still or by hitting the reset button.
• Use the middle mouse button to translate the view right/left and up/down.
• Use <shift> left button and drag up/down to adjust the scale.
• It is a good idea to leave the view stationary because on slow machine the moving 3D display can lock out other operations if many domains are displayed.

Adjusting the View Angle:

• In one of the view windows press the toggle button on the "Controls" frame - the dialog should now show the angle controls and a few more buttons and choice menus.
• Adjust the "Pitch" slider - the view should change (you may need to resize the dialog to avoid the need for scrolling) and the bounding rectangle in the navigator window will "tilt" to reflect the new angle.
• Adjust the "Yaw" angle to obtain a completely arbitrary orientation.
• For a given Pitch and Yaw adjust the Distance and observe how the section cuts remain parallel.
• The "Scale" option menu can be used to set the scale directly as an alternative to the "mag+/-" buttons.

From Pixel to Anatomy Component

• With the cursor within the view window click with the middle mouse button on a pixel - two lines of text will appear in the feedback window just above the view window.
• The first line gives the 3D coordinate of the voxel (x, y, z), the grey-value of the pixel and the current designation as a painted domain (with no doamins displayed it should say "greys").
• The second line is the component full-name as in the anatomical nomenclature database - the specific component name is on the right-hand-side with its containing components written to the left.
• To see the full name all the way from the top of the hierarchy click in the text window and move the cursor left with the arrow keys.
• With the cursor in the view window click the middle mouse button and drag - the text should update interactively with the movement of the cursor.

Displaying Anatomy Components

• From the "Anatomy" menu read in a component domain which are signified by a menu entry with the word "domain" e.g.: Anatomy->embryo->notochord->notochord domain, or Anatomy->embryo->organ_system->nervous_system->central_nervous_system->future_brain->future_brain domain
• The requested component will show as a red transparent overlay in view window (if that component is visible) and as a set of red bounding polygons in the navigator window.
• Clicking the "filled 3D view" toggle in the view window now gives a very effective view in the navigator window - try setting filled view on and adjusting the distance.
• "Tear-off" the "Domain" menu (above the navigator window) by selecting the dotted line at the top of the menu - the menu should stay on the screen within its own window border.
• similarly "tear-off" the "Select" menu from the "Domain tear-off" - this should show the number of independent domains available and their colours within a radio-box style (i.e. only one buttoin pressed at a time) menu.
• Press the darker blue button - second from top, probably labelled "domain_2.wlz"
• Read in a second component from the anatomy menu - this should now display in blue.
• Select colours and read in domains - note domains are added if the selected domain is unchanged.
• If you add multiple component together as one domain the section views will show the sum but the navigator window will only display the most recently read in domain - to force a 3D view of the combined domain toggle the "Display 3D domain" button twice - this will undisplay the selected domain then re-display it in 3D.

System Requirements

At the MRC we are investigating compiling the program within the Cywin environment for MS Windows machines therefore in the nearish future we hope to have a version that will run under windows 98/NT but this will require the user obtaining a X-Server to run on the same machine.

With this preamble, binaries can be provided for machines/operating systems:
    Sun Workstations/Solaris 2.6+
    Intel worstation/Solaris 2.6+
    SGI/IRIX 5.3, 6.4

If anybody has the means to compile code on other Unix systems and has the required Motif (1.1+) and OpenGL libraries then please contact the Mouse Atlas team and we may be able to transfer code to be compiled for more flavours of machines and operating systems.

For reasonable operation of the program the machine needs at least 64 MBytes RAM, 8-bit display (24-bit for some functions of MAPaint) and a CD-ROM reader.