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The current version of the morphology editor is cvapp1.1 (98-07-17).

Structure editing and conversion with cvapp

When it starts the editor loads a very simple cell with five branches. This can be used to explore the facilities in cvapp. A large set of structures of real neurons is available at http://www.neuro.soton.ac.uk/cells/index/topindex.html.

Reading and writing

To read and write files locally, use the open and save as... options in the 'file' menu. To read files across the web, enter the address of the server in the top row, and click the fetch list button to get a list of available data. Individual cells can them be chosen from the menu on the far right.

cvapp1.09 format compatibility
format read write
Neurolucida binary no no
Neurolucida ascii yes no
SWC yes yes
genesis .p no yes
neuron .hoc no yes

The SWC file format is used by the archiving software, and is the first to be fully supported for this reason.


Viewing styles

The editor supports four styles for presenting neurons. The nodes button can be used with all of them to show all the points in the data as well als the lines between points. The style is selected with the menu on the second row.
Skeleton projection
A single thickness line for each segment. This is the quickest way to draw the cell and so gives the best response time for large data sets.
Area projection
Each segment is drawn as a tapering cylinder with parallel ends, where the widths are the true values of the widths associated with the points at the ends.
Skeleton red-green stereo
A red-green stereo picture of the cell. You need red-green glasses to see it. The apparent depth is controlled by the slider at the bottom.
Area red-green stereo
as for skeleton red-green but showing the segment widths too.
The reverse button applies only to the red-green styles. It switches the 3-d effect from black + red + green to white - red - green (ie, magenta, cyan, blue).

The style menu contains another choice, file header, for editing the header of the file. Certain fields are automatically provided in the header for use in indexing archived cells, but anything else of interest can be included here too. Every line should begin with a '#' to distinguish it from the data.

One further viewing style, not accessible in this meny, is used in grow mode which shows more information about individual points. Whenever you leave grow mode the style reverts to that selected in the menu.


Panning, turning, zooming

To turn the cell in 3 dimensions, hold the right button and drag the mouse. It behaves as though you were pushing the front of a ball pivoted at the centre. The rotation menu selects between continuous echoing of the whole structure, or of just a cube. Unless the cell is very complex (~ 10,000 points) the continuous mode is usually most convenient. The midle mouse button (or any button with the SHIFT or CTRL keys) rotates about an axis perpendicular to the screen.

To move the image on the screen, click-drag-release with the left button. The image is shifted by the distance you drag.

To change the viewing scale, click with the left or right buttons without dragging. Left to zoom in; right, or long clicks with the left, to zoom out.

If you click and drag the mouse off the window and then draw loops the image scales continuously: clockwise to zoom in, anticlockwise to zoom out.

In summary:

Short clicks with the left/right mouse button
zooms in/out, keeping the point under the cursor fixed. Long clicks with the left button also zoom out.
Left button: Click, drag, release
Pans the display, so the point of the data at which you clicked is now where you released the button. (note, there is no echo as it drags).
Middle button (any with SHIFT or ALT): Click, drag
Turn the cell around an axis perpendicular to the screen. You get better control if you click near the edes of teh display.
Right button: Click, drag Turn the cell as though you were holding the surface of a ball, free to move about its center.

Shrinkage correction

The shrinkage correction item in the file menu brings up a window for applying a shrinkage correction to the whole cell. The editor keeps track of successive shrinkage corrections (using the SCALE field of the file header - don't edit it by hand!) so the values entered in the shrinkage correction window are not cumulative: they are always relative to the originally digitised data. If you set them to 1.0 in each direction you get back to the original size.

Editing, labelling and tracing

All the editing operations relate to the normal viewing styles except for add floating which belongs to grow mode.
trace
Highlight all points connected to a chosen point. Click a single point. All connected points will be highlighted. In a properly connected cell, everything should be highlighted - if any regions remain white, look for the nearest yellow section and join the missing link.
clear
Reset display, removing any highlighting. If in grow mode, return to normal mode.
join
Join two points. Click the two points to be joined in turn. As a side effect, all points connected to those joined are highlighted.
nodes
Toggle display of nodes as well as lines.
clean
Remove zero-length branches. This is important for some modelling packages which don't like segemnts of zero length in their structures.
cut
Break a connection. Click on two adjecent points. If nothing happens, the points probably arent adjacent. There may be two superimposed points at one end - try the clean function to get rid of zero length branches.
add between
Add a point in the middle of a section. Click on two adjecent points.
remove
Remove points one by one.
loops
Highlight any closed loops in the structure.


Making selections

section
Click on the extreme ends of the section. All points on the pathe between them will be selected.
tree
Click on two points in the 'trunk' of the desired tree, lower one first. The first point and all branches beyond in the direction fo the second will be selected.
points
Click the chosen points one by one.


Acting on selections

delete
delete selected points (and hence the lines between them).
mark
mark selected points according to the type indicated below the mark button. Clicking on the as .... label brings up a menu of predefined types. Alternativelty, enter an integer type in the box at the bottom.

"Grow mode" - adding and moving points

All the above operations relate to the normal viewing mode. To enter grow mode, use the check box in the upper right. To leave it, use any of the above function buttons (clear has no adverse side effects) or click the normal checkbox.

In grow mode, you can add new points, move points or change their radii. The add floating button adds a new point where you next click the mouse on the cell window. All other operations require the mouse alone.

When not over a point (echoed with a red circle) the mouse operations are as for all the other viewing styles. When on a point, the effects are:

make a new new branch hold left mouse button and drag
move an existing point hold middle mouse button and drag, (or CTRL or SHIFT with any mouse button)
adjust the radius of a point hold right mouse button and drag

Note that to correctly position new points in three dimensions it will be necessary to turn the cell from time to time move them in a different plane.


File formats


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Last modified: Fri Jul 17 15:34:22 1998