File Based and Input stimulus

The point of these stimuli is that they do not follow some regular pattern like a sine, linear, or pulse stimulus would. Because it is not regular, NCS needs to use an external source of information to determine when to apply stimulus to a given set of cells.

Required elements from the Stimulus Input Block:

How it Works

New data is read in at the start of the Time Increment. The data is different depending on whether the stimulus is File based or Input, but regardless, the data is scaled so that a cell's firing rate falls within the Dynamic Range set by the user. Diagram Example Stimulus
The Time Increment is divided into Fire Windows which last 0.0025 seconds. Each cell throws a new random number at the start of a Fire Window and compares the number thrown with the converted data. Any cell with a random number less than the converted data gets to integrate the stimulus. This integration lasts for Width seconds as input by the user.
For example, an Input stimulus receives the number 0.5 on its port which is then converted to a probability of 0.125 that a cell will integrate the stimulus at the start of a Fire Window. Cell 1 throws the random number 0.034, so it gets to integrate the stimulus, but Cell 2 throws 0.784 so it does not.

Converting Data to Probabilities

There are two major influences to the probability of firing, Dynamic Range and data read from the file/port.

Dynamic Range

In the input file, the user specifies a Dynamic Range for integrating stimulus. In a given second, a cell would be expected to integrate the stimulus at least at the minimum rate, but no greater than the maximum rate. For example, if the Dynamic Range was given as from 20 Hz to 80 Hz, then a cell should integrate the stimulus at least 20 times in one second, but no more than 80 times in one second. So, if the only time a cell has the option to integrate is at the beginning of the Fire Window, and a Fire Window last 0.0025 seconds, then a cell will integrate with probability equal to 0.0025 times the current value from the dynamic range (i.e between 20 and 80 Hz). That current value is chosen based on the data.

Data Read

In order to determine whether the cell should use the minimum Dynamic range, the maximum Dynamic range, or somewhere in between, the data is examined. In the case of file based stimulus, the entire file is read in and the maximum and minimum data value are discovered. These extrema allow every individual data value to be scaled to a number from 0 to 1. This scaled value then corresponse to some percentage of the dynamic range to use. That is, 0 means that the minimum range should be used, 1 means the maximum range should be used, while 0.5 would mean to use a range in the middle.

For input stimulus, there is no way for NCS to know what the largest and smallest values would be, so it assumes that it will read an already scaled value (0-1) off the port, then select the daynamic range from that.

Integrating Stimulus

Once the data has been converted and the approiate dynamic range selected. The probability is calculated and each cell throws a random number. Cells with random numbers less than the computed probability get to integrate the stimulus. These cells will now use the AMP_START and WIDTH properties of the stimulus.

Amplitude

When the stimulus is integrated, the value contained in AMP_START is sent to the cell. The stimulus can be set to either of two modes: CURRENT or VOLTAGE.
CURRENT
The amp specified is added to electrical current from other sources (Channels, Adjacent compartments, etc.) so that the sum of all currents can be use to affect the cell's membrane voltage.

VOLTAGE
The amp specified bypasses all other electrical current and sets the cell's membrane voltage to the same number (i.e. The stimulus is treated as a voltage value and not as an electrical current that must be mathematically transformed into a voltage)

Width

The stimulus will be applied for a certain number of timesteps before it shuts down and waits for the next Fire Window. The user will specify how many seconds this Width should be.

Customizing Stimulus Further

The example given so far have shown only one value being read from the file or read off the port in order to determine if a cell will fire. Using FREQ_COLS and CELLS_PER_FREQ, more values can be sent to NCS to add more variance to the firing rate.

Frequency Columns

This just means how many different values (frequencies) will be read in at the start of the Time Increment. For example, an Input stimulus can declare three FREQ_COLS and send 0.12, 0.78, 0.43. Some cells will use the first value to establish a probability of integration, while other cells will use the second value. And a third group of cells will use the final value.

Cells Per Frequency

This determines how many cells are assigned to each frequency. Since there is only one number in CELLS_PER_FREQ all frequencies will have an equal number (so a single frequency can't have 10 cells while another frequency has only 5). If there are not enough cells to split between the frequencies, that is an error. If there are cells left over after dividing them among the frequencies, those cells will not be included.
Example: There are 20 cells and 3 frequencies. If the user wants 7 cells per frequency, that is an error since there need to be 21 cells (3*7=21). If the user wants 5 cells per frequency, then only 15 cells are assigned to a frequency while the 5 left over cells will not be included in stimulus integrartion. Diagram multiple frequencies