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A single point in a trajectory.
A MapIDTag is can be included in a BoundaryMap object (eg, when capturing a set of points and boundaries) to attach an identity tag to the map. This is in addition to the map's name. IT is used, in particular, for database queries where the ID tag is sent in the query to identify the map for which data should be returned. That is, the ID tag should be the string by which the map is known to the database.
A boundary map is a collection of nodes, _CMLINK(map, MapPoint, MapPoint), links, _CMLINK(map,MapBoundary,MapBoundary), and labels, _CMLINK(map, MapLabel, MapLabel). The regions in the map are deduced from the nodes and boundaries by the software and labels are assumed to apply to the region they are in. The man use of the map editor is to construct a map (from which the regions can be deduced) starting with an image or picture (from which the software is not smart enough to deduce the regions). This involves placing points at each intersection of region boundaries and also sometimes at inflections in a continuous boundary, and then conecting them with curved lines (the MapBoundary objects). The curved lines attach at each end to map points, but the middle point is free, allowing a adjustment to make them fit curved boundary sections. The first step in digitizing a map in this way is to load an image in the background of the editor by specifying the desired image file in the _TT(image) field. It is well worth massaging the image with an image editing program in advance to simplify the digitization process. The most important features for a convenient image are that it should be small (a few hundred pixels on each side) and smooth (greyscales, not black and white). Blurring often helps to keep the map readable when reducing its size. It is also convenient to reduce the contrast, for example to use a light gray background with dark gray writing. This way one can see both the map and the points and boundaries being placed on top of it. The advangages of small images (small numbers of pixels) is that they are quick to draw, even when blown up so only a small part is visible on the screen. If the graphics performance is poor, it may well be that the oiriginal image has too high a resolution. Once the image has been converted to a suitable format and loaded in the editor it will be drawn in the background occupying an area of width specified by the _TT(imageWidth) parameter. This is a dimensionless quantity, which serves to relate the size of the image area to the size of the points being placed on it. In these units, the diameter of a map point is 1, and the default length of a boundary section is 2. A value of about 20 is often conveneint for the _TT(imageWidth) but this depends on how detailed the final map will be. The map is actually made by dragging items off the bar at the top (click map to display them if necessary) and positioning them over the image. The boundary lines will stick to points, but not vice versa. To detach a boundary line, click and drag with the right mouse button. Draging the points at either end will move just those points. It is often easiest to start at the bottom of the map and build upwards so as to avoid new boundary sections sticking on to points at the top as they are dragged past. The view in the window can be adjusted in any of the _CMLINK(../.., panzoom, standard ways). As yet (January 02) the main reason for digitizing maps this way is for use with the _CMLINK(map, CoCoMacBrowser, CoCoMac browser). This requires a tag to be associated with each map giving the name by which it is known in the database. The tag should be entered in the _TT(cocomacID) field. For the map IDs, CoCoMac uses the first letters of the authors surnames followed by the year of publication (two digits), as in B09 for the Brodman map published in 1909. Labels can be added to the map by dragging off label items from the top and setting the string to use in the label in the box on the right hand site. For use with CoCoMac, labels should correspond to the terms used for each area within cocomac. These are the terms used by the original authors in the text and may differ in some cases from the labels used on maps. The _CMLINK(map,CoCoMacBrowser,CoCoMac browser) can be used to get a definitive list from CoCoMac for any given map. Finally, the map editor lets the user visualise the regions in the map with the makeRegions button. This extracts the periemters of all closed regions and displays them in a _CMLINK(standard,DisplayListEditor,DisplayListEditor). The regions are colored according th the _CMLINK(standard,ColorTable,color table) set for the _TT(lineColors) in the display list window, so it may be necessary to create a new color table before anything is visible. Note that new color tables default to grey scales beginning with black, so the map may still be hard to see - the randomize option on the color table should generate more useful colors for displaying maps.
A single point in a trajectory.
A map with cotiguous labelled regoions specified by their boundaries. For details see the _CMLINK(map, BoundaryMapEditor, BoundaryMapEditor).
A box for capturing compound cell objects. See the _CMLINK(assembly, CaptureBox, capture box) for details. The only extra feature of this component is that once captured the compound is called a _CMLINK(network,Neuron,Neuron) so it can be used in populations of neurons.