Using CVAPP with GENESIS

Dieter Jaeger

Emory University

CVAPP is a morphology viewer/editor written in Java by Robert Cannon for converting between file formats. The original version (1.1) and a modification by Steve van Hooser to handle remeshing of structures for GENESIS (1.4.3) are available at http://www.compneuro.org/CDROM/docs/cvapp.html. More information about CVAPP, with a link to basic usage information can be found at http://www.compneuro.org/CDROM/nmorph/cellArchive.html.

Dieter Jaeger has written the following supplemental notes for using version 1.4.3 with GENESIS:

Directions on using CVAPP to convert Neurolucida v3 files to GENESIS 2 cell parameter file (.p) file format


     Step 1: Reconstruct cell in Neurolucida v3.x

     Be careful not to miss any dendrites or misjudge diameter of thin
     processes. Save data in ascii format.

     Step 2: Install cvapp on your computer

     The meshing facilities required for genesis are only available in
     the version 1.4 or later of cvapp. If you are using Linux, set the
     CLASSPATH environment variable to point to the directory
     containing your cvapp installation.

     Step 3: run cvapp

     In the directory containing you Neurolucida data asci files, type
     java cvapp.

     Step 4: File -> Open -> > your file >

     Step 5: Replace the soma

     GENESIS uses a single spherical compartment as a soma instead of
     the polygonal shape used by Neurolucida. Delete the existing
     polygon with select tree option, followed by delete. To select a
     tree, click two points on the soma contour after clicking the
     select tree option. If the soma was not a closed shape (as it
     should be), you need to start the tree selection at one of the
     contour endpoints. In general after clicking on a menu command,
     further instructions will appear as text in the upper left corner
     of the cell display.

     To create the new spherical soma, use menu option add floating to
     add a single compartment in center of intended soma. Drag out the
     size of this compartment w/ right mouse button. Delete the narrow
     end of the created cylinder by using remove menu option and left
     clicking on this point. Now only a single point is visible for the
     new soma, but the diameter information is retained. If you don't
     see anything left of your soma, click on the nodes menu item. This
     toggles a single point visibility mode. Remove old soma.

     Step 6: Connect dendrites to new soma

     Click on ident menu option, then left-click on the trunk
     compartment of a dendrite, then left click on the soma point. A
     connection will become visible. If it doesn't, click once on the
     outlines toggle, which makes connections visible as yellow lines.
     Repeat this process for each dendrite, starting with a new click
     on ident.

     Step 7: Mark areas of the cell as dendrites, axon, soma etc.

     Use the trace select option to select pieces (selected pieces
     change color), use the pulldown menu located underneath the mark
     menu item (right click on text string starting with as) to set the
     desired structure type. Then click on the mark menu item.

     [Important note: If you need to create new types of structures,
     you need to add this to a file called a marking file (example see
     HN4_marks in your cvapp directory). You can add the structures
     from a marking file from the mark menu options.]

     Step 8 option 1: Save cell to genesis .p file w/o remeshing the
     compartment structure

     Use file -> save as -> genesis v2.1 option. DONE. Most often,
     however, Neurolucida files are not drawn with electronically
     correct compartment sizes. To recompartmentalize the cell
     (meshing), follow step 8, option 2.

     Step 8, option 2: Mesh the cell

     Beware, there is no undo option - any goof and you go back to step
     1. However, you can save the cell in its current state in cvapp's
     native format with the save as swc option and then reload it as
     often as you like.

     Set meshing parameters in the file -> set meshing parameters menu
     to reflect passive constants of your cell. (Comp. length is in
     electrotonic constants, max radius change is in microns difference
     diameter between beginning and end of a cylinder to be meshed
     together). Then mesh. You will get a text output in your console
     window as each dendrite is meshed, and you will get a final output
     Meshing Done; number of compartments: xxx. This process can take
     several minutes with large neurons. If you get errors, most likely
     your soma isn't connected right, or you have stray points in your
     file. Start over and try to eliminate such extra points. When the
     meshing works you will see nicely regular spaced node points
     appear in the drawn cell. Then follow Step 8, option 1.