README file for etonic.c and dendro.c
                           Alex Protopapas
                               2/21/96

etonic.c

This program will ascribe electrotonic lengths to the segments of a compartmental model. It is to be used with GENESIS .p files (GENESIS parameter files which describe single cell properties). The usage is as follows:

            etonic [resting .p file] [Rm file] [outfile.p]

The ".p morphology file" refers to the .p file for which electrotonic lengths are to be calculated. The .p file does not have to be doctored in any way (i.e. comments removed, etc.) before it is used by etonic as an argument. The "Rm file" must be generated by your GENESIS scripts. It simply contains Rm values from all the compartments in the order that they are listed in the .p file. This is what an "Rm file" should look like:

                           7.097508619e+14
                              2968144128
                           2.312419123e+10
                           1.142296084e+11
                            1.00795351e+11
                           4.299717018e+10
                           1.015382753e+11
                           4.329560064e+10
                            7.08895785e+10
                           5.508040294e+10
                                  .
                                  .
                                  .

The "outfile.p" is the name of the GENESIS .p file that will be generated by etonic. The lengths of the compartments in this file will all be electrotonic lengths.

The usefulness of this program lies in being able to visualize changes in electrotonic length in an anatomically realistic way. For example, say you want to compare the electrotonic structure of a neuron in the presence and absence of background synaptic activity. You may do so by generating "Rm files" in the presence and absence of background activity and the compare the resultant electrotonic structures. This will give you an idea of "how electrotonically far away" different areas of the dendrite are from the soma. For a more thorough explanation of the concept of electrotonic length, see the comments in etonic.c.

The program "etonic.c" is entirely self-contained. To compile, simply type:

cc -o etonic etonic.c -lm -[flags of your choice]

The program is pretty well documented so it should be pretty easy to make any changes that you deem appropriate. Comments within the program give further information about electrotonic lengths and why you might want to view the cell structure in this manner.

dendro.c

This program does essentially the same thing as etonic.c, except that it generates a dendrogram instead of an anatomically correct .p file. Dendrogram representations are useful for quickly gleaning information about compartment connectivity and electrotonic structure without having the details of anatomical structure to obscure things.

The usage is as follows:

dendro [.p file] [Rm file] [dendrogram output file]

The "dendrogram output file" can be visualized by the software tool of your choice. I generally use MATLAB for this purpose, although you could easily write a script in GENESIS to serve the same function. I have included a MATLAB script in this directory which will display the dendrogram output files appropriately.

To compile:

cc -o dendro dendro.c -lm -[flags of your choice]

display_dend.m

This is a MATLAB script which displays dendrogram output files.

FUTURE:

In the not so distant future, these utilities will be incorporated into the standard GENESIS release.