# 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.