The name of the visualization tool is visu_nbc. Visu_nbc is a tool to visualize biologicals neurals networks activity. This tool is also accessible from the xnbc menu : Applications->Visualization
To visualize the network connectivity, visu_nbc needs the files decribing the connectivity matrix (*.len and *.wgt). To visualize the evolution of the network activity, visu_n_b_c needs a a .def (simulation definition) and a .pmb file (menbrane potentials).
Four representations are available. They are accessible either using the Option/Type of representation menu, or more directly by pressing one of the four pushbuttons in the menu bar. These representations are:
This representation is like a dot display but shows as a color graph the evolution of the menbrane potential between spikes (Fig. 9.1). Each colored square represents a neuron. Each column represents one iteration of the simulation. The black lines delimit clusters.
With this representation, it is also possible to select one of the neurons with the pointer and to depress the right mouse bouton to have a representation of the intra celllular recording of the selected unit (Fig. 9.2). The time scale ca be zoomed at will by selecting with the mouse middle bouton 2 limits. The right mouse bouton go back to the original scale.
This representation displays for each cluster its global activity in percentage at each iteration (number of spiking neurons / number of neurons in the cluster) (Fig. 9.3).
This representation displays for each selected unit the temporal evolution of the membrane potential (Fig. 9.4).
This representation displays the network state at each iteration. The network is represented like a matrix. Each colored square represents a neuron. Each black big square represents a cluster. Small lines represent connections from a neuron to another. With Show Details connection types can be visualized. When a neuron fires the spike can be seen travelling along its axon toward others neurons (Fig. 9.5).
Open Network Files : choose a .cnx file.
Open Simulation Files : choose a .def file.
Close Simualtion : close simulation files.
Exit : exit visu_n_b_c.
Show Details : visualization of details for the selected. representation (Button On/Off).
Refresh Screen : redraw the selected representation.
Print Network : print the selected representation.
Scale Top Value : permits to change the top value of the menbrane potentials color scale.
Time Step : permits to modify the time between the visualization of each step of the simulation.
Type of representation : u cascaded menu allowing to select the type of representation. It is a duplication of the pushbuttons on the menu bar. Linear: color dot display with the membrane potential reprented by a color
Matrix: representation of the neurons on the diagonal with their connections with the other neurons. Spikes are seen travelling on the axons (small red bars).
Global Activity: Activity of clusters (not of nuclei!) represented by the percentage of simulataneously firing units in a given cluster. Membrane Potential: Active only if at least one neuron was selected. Represents the intracellular recording of selected neurons.
Browse manual: self explaining.
About Visualization : General informations.
This scale associates a color at a value of the menbrane potential. This scale has two parts :
The first one (red rectangle) indicates the potential for a spike. This value is read in the .def file.
The second one indicates a linear correspondance between color and potential values. The top value can be modified (the bottom value is read in the .def file as the Negative Reversal Potential). By increasing this value, small variations of the potential can be filtered, and on the opposite by decreasing it small variations of the potential around the resting potential can be magnified.
To change this value :
- select the corresponding menu in the Options menu.
- move the cursor of the scale in the dialog box to set the wanted value.
- click on Ok to change the value or on Cancel to keep the previous value.
The time between representation of each step of the simulation can be modified. This time acts on the visualization speed not on the simulation time step increment. The major purpose of this function is to slow down the visualization when the network is small or the computer too rapid.
To change this time :
- select the corresponding menu in the Options menu.
- move the cursor of the scale in the dialog box to set the wanted time.
- click on Ok to change the time or on Cancel to keep the previous time.
These buttons are in the bottom left corner of the window. They control the visualization like a video tape player.
The first button at left stops the visualization and returns to the first iteration.
The second button starts the visualization.
The third button pauses the visualization at its current iteration. Visualization can be restarted from this iteration by clicking the second button.
The fourth button allows to go directly to a specific iteration. Enter the selected iteration number in the iteration text field, then press return or click on this button to go to the selected iteration.
The fifth button runs one step of the visualization (step by step visualization).
Several fields display informations on the window.
Iteration : display the current iteration. This field allows too to enter an iteration for the "Goto Index" button (see previous section).
N.G.A. : display the Network Global Activity in percentage (number of spiking neurons / number of neurons in the network).
Network Information : display number of clusters and neurons in the network.
Special Informations : display differents informations according to the selected representation. To obtain this information click in the window where the visualization is displayed. Then a hair-cross cursor, moving with pointer device, appears in the window. Move the cursor to point on which part of the visualization informations are needed.
Print Network
To print the visualization at its current iteration (when the visualization is paused) select the corresponding menu in the Edit menu.
Then choose the PostScript printer, if the file must be kept or not after printing, the type of the printed part: entire representation or only the visible part (what is currently seen in the window). Then click on Ok to print or on Cancel to cancel it.
If the PostScript file is kept for further printing, a specific file name can be given (default name is file_name.ps.
Open Files
To open Network files and Simulation files select the corresponding menu in the file menu. Then select file in the dialog box and click on Ok to open it or on Cancel to cancel it.
visu_nbc is like a "video tape player".
A normal session is as follow :
- Open Network file (.cnx) then the representation of network appears in the window. Default representation is LINEAR REPRESENTATION (see below).
- Open Simulation files (.def). visu_n_b_c tries to open the given file name with .def and .pmb extension. If it fails the visualization is impossible and an information message is sent. A file name without extension, with a .def extension (default int the file selection box) or with a .pmb extension can be given.
- Now the visualization is ready to start.
- At every moment the representation type can be changed, or special informations on the current simulation can be obtained.
- To print the network, change time step or change color scale top value, the visualization must be paused.
- At the end of the work, close the simulation.
- Others Simulation files for the same network or an other network can be obtained.
Using the second (MB2) and third (MB3) mouse boutons, it is possible to quickly select or obtain a membrane potential recording.
The MB2 allows to directly select neurons on the linear representation. If not already visible, it displays the neuron selection/unselection box. It has the same effect as if going through the menu.
When the file reading is completed, it is possible to directly obtain a small window with the membrane potential of the neuron selected using the MB3. WARNING: the plot begins a time 0 and finishes where ou selected the neuron. If the MB3 is depressed in the middle of the panel, you get only from 0 ms to about the half simulation time; thus, selection should be done at the right part of the panel. The choise of a subpart of the trace is possible in the panel using the MB1, MB2 or MB3. MB1 is used to set the limits of the part of interest (a vertical red line is drawn at the chose place, and can be displaced while the mouse button is pressed). Red lines can be drag using MB1 again. When the limits are OK. MB2 zooms the part of interest (the window is rezible at will). Zoomed view can be rezoomed at will. MB3 goes back to the original.
A button Print allows to print the membrane potential.
A button Cancel closes the window.
Up to six neurons (windows) can be visualized simultaneously in this way.
Input: *.len, *.wgt, *.lnk
Output: *.ps
No known problems.
