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Directions on how to use cvapp to convert Neurolucida v3 files to Genesis 2.1 .p file format

Dieter Jaeger

General Notes:

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.