models/chapter8

fig83a	Simple cable witha 1ms current injection and recorders at each end. The voltage transient is biggest at the injection site. To change the site, press (and hold) the right mouse button on the white current injector. It will become detached, and then can be connected to another node. Cell properties can be varied with the sliders. To change the cable, use the left mouse on a node to move it, the middle one to add a new segment, and the right one to change its diameter - all with press-drag-release operations. For more details, see the BranchedCellEditor page. The current injection is shown on the lower right. Details of how to midify it can be found under the ProfileEditor.
reciprocity	Reciprocity. There is a current injection at the site of the white injection marker. The graph shows the voltage transients at the injection site (green) soma(red) and another dendritic site (blue). Remember carefully the blue transient. Now detach the white current injector (press and drag with the right mouse button). Once it is free drag its injection site to the site of the blue recording, avoiding other points or it will stick on the way. Now the green voltage transient at the original injection site is exactly the same as the original blue one. This only applies for the injection and recording sites. To verify that it is an exact agreement, use the keep in background option under the data menu to keep one set of results in the graph while moving the injector.
shunting	Shunting during an extended current input. Each point reaches a plateau where the persistent leak matches the input, but the potentials are widely different depending on the local load. The narrow sealed end (blue) ends up at about the same potential as the wide soma: its load is lower but the resistance is higher. Note that the y axis is considerably expanded. You can change the diameter of a point by clicking it with the right mouse button and dragging the mouse up or down.
frequency	Frequency dependent attenuation. The input square wave can be stretched or compressed by dragging the last pink circle on the lower line. Higher frequencies show more attenuation, but if the potential saturates (e.g. reduce C-mem to 0.5 or so) then frequency has no effect.
numerics	Discretization in space and time. Change the timestep between about 0.01 and 1.0 to see how the accuracy of the results varies. For large timesteps, individual segments of the response are visible as straight lines. Note however that even when the results look angular, they are qualitatively correct. It is often easiest to work with large timesteps most of the time, only a few times smaller than the shortest event, and only use small steps when quantitative results are required. Likewise, the space discretization can be changed with the dsqrtr parameter (Delta Square root of r - the amount the integral of the square root of the radius has to change before inserting another point. Small dsqrtr means a lot of points - accurate but slow; large means that only the points in the structure are used.
transforms	This is the cell used for the transforms. It is an instance of the BranchedCell object, but the default view does not let you add or remove segments. Instead, there is a pink dot which sets the origin for the transforms. Clicking on the structure moves the origin. Thus, for example, to see the attenuation between dendritic sites, move the origin to one of them and the color coded transform will give the attenuation to or from that siite to each point on the cell. To change the geometry of the cell, click the modifiable checkbox and you can edit it just like the other examples in this chapter. You can also import cells with the import option from the menu at the top but they must be in the .swc format used by the conversion program cvapp. All the cells in the Duke-Southampton archive (included on the CD and web site) are available in this format. Passive propagation and morphoelectrotonic transforms. The graph in the middle shows a simple cell color coded according to the log voltage attenuation from the soma for a sinusoidal signal of angular frequency omega as given in the left panel. Change the cellular properties - membrance capacitance, C-mem, cytoplasmic resistivity R-cyt and leak conductance G_pers to see how they affect attenuation. The graph shows the attenuation to in the dendrites of a somatic signal. To see the converse, change the transform option to V_attn_cp - the centripetal voltage attenuation. The colouring at each position then indicates the attenuation at the soma of a sinusoidal signal applied at that position. An alternative way to display the data is available as the scaled option under the display field. In this case the length of each segment replaced by its log attenuation factor but its direction is kept the same. Use the find button to recenter the graph. The origin used in the transform is shown by a pink dot on the cell. This can be changed by clicking another point on the structure. The cell can be edited with the BranchedCellEditor by clicking the modifiable checkbox.