MacOStat is an application designed to browse three dimensional brain atlases; it operates on MacOS (and is compatible with both OS 9.x and OS X). With MacOStat, you can view slices from an atlas at any plane you desire, reslice the atlas into as many individual slices files as desired, and align sectional material for later assembly into new atlases.
To browse an atlas you will need a Macintosh computer equipped with MacOS 9.0 or later, and the CarbonLib 1.3 extension. You will also need a large amount of RAM. For OS9, we recommend a minimum of 128MB of physical RAM, with virtual memory set at 256, or, for better performance, at least 192MB of physical RAM. We have found that an iMac computer equipped with enough memory makes a good station for atlas browsing; we have also successfully browsed our mouse atlas on an iMac with only 64MB, and virtual memory set to 192MB, but navigating the atlas is slow
Start by copying the MacOStat application to your hard disk. You can not run MacOStat from a CD-ROM, as it needs to create some setup files. It's best to create a folder just for MacOStat. The first time you run the MacOStat browser, it will ask you where your "VOI Selectors" folder is. You won't have one, so just cancel the dialog box, and MacOStat will create one in the same folder as the MacOStat icon is found.
Also, you'll need to have a version of Apple Computer's CarbonLib extension installed in your Extensions folder, if you are using MacOS9.x You can get a copy of this extension (it must be version 1.3 or later) from Apple's website. Click here ftp://ftp.apple.com/developer/Development_Kits/CarbonLib_1.4GM_SDK.img.bin to download an archive file which contains the appropriate library.
MacOStat and Neuroterrain
MacOStat is an atlas browsing application. It allows you to examine 3D data sets at any arbitrary angle, align sectional material to a 3D dataset, reslice the dataset at any arbitrary angle, and view volumes of interest. The 3D data sets that MacOStat works with are called Neuroterrain files.
As a general note, in this user guide Neuroterrain files are usually referred to as atlas files.
What are Neuroterrain files?
Neuroterrain files are a complex mixture of 3D gray scale data, volumes of interest and related metadata, along with scaling and coordinate conversion data. At the present time, it is not possible for you to generate your own Neuroterrain files, but we can produce files for you if you provide us with the base images. Please contact us for more details.
Loading an atlas
Load or open an atlas like you would any other document - double click on the Neuroterrain icon, drop the icon on the Neurocartograher icon, or use the Open item from the file menu. MacOStat will first ask you whether you want to view volumes of interest as shaded areas or outlines, and will then load the file into memory. Neuroterrain files are large - you will need to be sure that you have allocated sufficient memory to MacOStat; the default setting is about 130MB. This is usually enough for a 18µm mouse atlas.
Browsing more than one atlas
It is possible to browse more than one atlas or Neuroterrain file at a time. If you use the Open command from the File menu, each will be in its own window, and will operate independently. If, however, you use the Place command (from File) for the second atlas, it will be opened in the front most atlas window. Now the atlases will operate together. Navigating in one results in both being updated, we call this conavigation. Only one atlas in a window will have "focus." The atlas with focus will be the dominant one, and any VOIs displayed will be those of the dominant atlas. More on this later.
Navigating by mouse
The easiest way to navigate through the neuroterrain is visually, using the mouse. The screen display updates in real time, and both coarse and fine adjustments to position are possible.
Moving the virtual knife
The location of the slice displayed is controlled by the virtual knife. This is moved by selecting (clicking on) a movement icon in the control palette, then dragging the mouse (with the mouse button down, of course) horizontally on either the wireframe window or the atlas window. Controls are provided for rotation in any of three principle axes, and for movement along the slicing axis. There are also controls to select the slicing axis (for coronal, horizontal and sagittal presentations), and to reset the virtual knife to the middle of the current slicing axis.
As you drag the mouse, not only do the wireframe and slice display move, but the orientation data in the upper left corner of the wireframe changes to reflect the virtual knife location.
If you have multiple atlases in a single window, only the atlas having focus will update, until the mouse button is released. At that point, all the other atlases will update. You can change the atlas focus by clicking on another atlas, which will then have focus.
Changing slicing angles
The virtual knife can be rotated about any of the three major axes. You control the axis of rotation by clicking on the appropriate icon in the tool palette. You can only rotate about one axis at a time.
Remembering locations
As you navigate through an atlas, you may find that you want to return to a particular position. You may tell MacOStat to remember that location by using either the menu command, or the "Mark" button on the wireframe window. To return to a remembered location simply choose it from the popup menu in the wireframe window.
You may also save these locations on disk so that you can load them again during another session. The "Save..." and "Load..." options on the popup menu allow for this.
Mouse Pointer locations
There are two numeric displays that are shown on the wireframe window. One, in green, gives the orientation of the virtual knife. The other, in red, gives the current mouse coordinates when the mouse is over the atlas that is in focus. If the atlas contains the necessary data for sterotaxic coordinate conversions, the units (mm) are displayed after the numbers, otherwise, the coordinates are given in unit-less, atlas-relative values.
Navigating by number
In addition to directly manipulating the display, you can enter coordinates for the specific slicing plane you want. To do that, you need to understand the coordinate system used in the MacOStat software.
The coordinate system
Coordinates used by the atlases and browser are based on an internal, atlas-relative system. The X-axis of the atlas is always defined to run from -1.0 to 1.0 units, no matter the size or resolution of the atlas; the Y-axis and Z-axis are then some multiples of this. The default presentation for the Neuroterrain files we supply is coronal, and here the X-axis is horizontal, and lies in the slicing plane; the Y-axis is then vertical, and the Z-axis runs in and out of the screen.
Entering coordinate values
The entry areas for slicing plane coordinates are revealed by clicking on the zoom box for the wireframe window. There are four entry boxes, one each for X, Y, and Z rotation angles (expressed in degrees) and one for offset along the slicing axis, in atlas relative values. The display updates as you move from one entry area to the next, either by tabbing to or clicking in the next area.
Volumes of Interest
One of the more useful functions of the MacOStat is to display volumes of interest. These are 3D segmentations, much like those in 2D printed atlases, but they may be sectioned in any orientation.
Displaying VOIs
The display of VOIs is enabled by a menu item. Each VOI may also be turned on or off separately, and can be made to appear dim or faded. To enable VOI display, choose "Draw Contours" from the "Volumes" menu. To choose individual VOIs for display, or to change between dim and bright display, choose "VOI Display...". Because it can take a long time to draw VOIs when navigating through an atlas, by default VOI display is temporarily displayed during navigating. You can turn display on during navigating if you wish. The menu item for this is also in the Volumes menu. When a VOI is visible on screen, positioning the mouse pointer over the VOI will result in the name of that VOI being displayed in the upper left corner of the view.
When conavigating, the VOIs for the atlas having focus will be displayed on all other data sets shown in the window. Clicking in different data sets changes the VOI display for all data sets.
VOI Colors
The color used to display a VOI is a user option also. Clicking on the color box at the right of the VOI selection dialog will bring up a color picker, allowing you to visually choose the color to be used for the VOI.
Saving VOI Display sets
VOI selection and color data are not normally persistent, but you can save these settings if you change them. To do this, select "Load..." from the popup menu in the selection dialog. Save them the same way, using the "Save..." item. These files are stored as tab-delimited text files, so you can also view them with either word-processor or spreadsheet programs, and modify them externally.
Reslicing an Atlas
The atlases may be resectioned at any angle; reslicing can be done to include volumes of interest. If your sectional material is aligned to the atlas slices, you can pass the segmentation to your material. This is useful for analysis with the MacOStat's sister program, Brain. To reslice an atlas, you must first be sure that the atlas is set to show outlines of the VOIs, and not shaded areas. You must then mark two locations, the positions you want to start and stop slicing. Then, choose "Reslice volume" from the "Slice" menu, to get the slicing dialog.
"Number of slices:" is pretty much self-explanitory., "Base name:" is the root name used for sliced files. You can choose anything you like. Slices are numbered sequentially, from the setting in "Number slices from:" An appropriate number of leading zeros is included to make the slice names appear in order when sorted by name in the Finder.
"Slice Subsidiaries" will slice all the data sets in a the window, not just the focused atlas.
"Include ROIs" will also slice any visible VOIs, and will add an outer contour. This outer contour is very useful when aligning your own sectional material to our atlas - it provides the target ROI for Brain to use.
Sliced images need to be put somewhere, and that somewhere is the folder shown in "Store slices in:" You may change this location with the "Choose folder" button.
We only provide for nearest neighbor pixel interpolation at this time; slice interpolation is different. "Bisecting Plane" is the average orientation between the starting and ending positions, while "Interpolate orientation" will spread the difference out among all the slices.
Finally, you can scale the slices to meet your needs.
Aligning Images
Once sliced, images from a data set may be used in our Brain application to align your sectional material. Using the align command in Brain will not only align the two images, but will also transfer orientation data to your images. These images can then be fed back into our reconstruction program to create new data sets. (See us for details.)
As a general principle, only trivial, uninteresting software is bug-free. We don't think MacOStat is either trivial, or uninteresting, and unfortunately, it is not bug-free, nor is it "complete." Here are some of the bugs and infelicities we are aware of:
The remembered locations popup menus don't work very well - if you have more than one atlas open, the locations appear in all the popups, and MacOStat gets confused, and sometimes crashes.
Occasionally, the MacOStat will crash on startup. This is usually related to the preferences file. Deleting this file will usually fix things.
As we fix problems, and release new versions, they can be found on our web site, www.neuroterrain.org.
