The main ninjaGUI interface

The following is a screenshot of a typical ninjaGUI user interface:

As the GUI was designed to be compatible with multiple hardware devices, not all functions might be compatible with all devices (and then they will be greyed out or disabled). Additionally, the number of sources and detectors displayed will be dependent on the number of them present in the device. This page will describe the different elements of the UI.

The probe diagram:

This is a schematic of the sources (red crosses) and detectors (blue circles) and their relative locations as specified in the .nsd file. For ninjaNIRS, the sources and detectors come in pairs, and that's the way they are represented in the diagram. However, even if they are present they might not be enabled. The grey lines are channels, and they always connect one source with one detector. The colored lines in the diagram are "active" channels. The currently active channels are plotted in real time during the acquisition. Note: all channels in the diagram are recorded during acquisition, but only the "active" ones are plotted in real time. The active channels can be changed by clicking one of the grey lines, which will change the clicked channel into "active", while "deactivating" the rest. We can also click on a source or a detector, which will make active all channels from that source or detector.

The current acquisition window:

This window plots, in real-time, the acquired signal from the instrument. It will only plot the "active" channels from the probe diagram. The color of the curves correspond to the color of the selected diagram in the probe diagram. Currently, the GUI is compatible with up to four wavelengths. Each wavelength is displayed in a different line style. When plotting intensity (digital levels) or optical density, the "red" wavelength is plotted as a dashed line, and the "infrared" wavelength is plotted as a solid line. When plotting in the chromophore concentration space, the dashed line is oxyhemoglobin and the solid line is deoxyhemoglobin. The GUI contains several options to alter how things are shown in this window.

Display options:

This panel shows several options to modify the display of the current acquisition. The "display window" field allows us to change the time span of the plot (always from the most recent sample to the window length before that). y min and y max are used to change the span of the y-axis; these will only work if the "Autoscale y" checkmark is disabled. Otherwise, the GUI will decide the y span automatically based on the maximum and minimum values on the currently displayed time span. The "display type" options decide the units of the plot. "dB" is the raw intensity (digital levels) in a logarithmic "decibel" scale calculated with the formula 20*log10(DL), where DL is the intensity in digital levels. This scale is useful for estimating the relative intensity levels of each channel, in order to compare different channels and see which ones have low intensities (usually associated with bad coupling to the scalp). The optimal levels are very dependent on hardware, but for ninjaNIRS optimal levels are between 130 and 180 dB for long separation channels. With DeltaOD, the data is converted to a difference of optical density. For this, the mean DL value of the data plotted in the time span is subtracted from the plotted data, and then the logarithm of the data is calculated. As this display type removes the offset, it is better to observe things like the cardiac cycle in multiple channels at a time. Generally, not being able to observe the cardiac cycle with a channel (when the subject is not moving) means the channels is poorly coupled to the scalp. Even when the cardiac cycle is observed, the less noisy it looks, the better the coupling is. Finally, the Hemoglobin option converts the data to change of hemoglobin compared to the mean of the window. This space is what is eventually used by other applications (such as Homer) to calculate the hemodynamic response function. Regardless of the display type chosen, the data will only be saved in digital levels (not decibels). The "wavelength display" box shows the wavelengths being captured with the system. By default, we plot all wavelengths. We can click on one of the wavelengths to plot just that one. If we want to display multiple wavelengths, we need to press on the additional ones while holding the "Shift" key on the keyboard. The "Plot data" checkmark determines if the data is plotted in real time. If unchecked. No plot will be produced (the data is still recorded normally). This option is mainly used if we want to optimize the performance of the app, especially for applications where precise timing is required (for example, when synchronizing EEG and fNIRS data is necessary). The Display aux toggle button is used to control if the acquisition window will display the fNIRS data (deactivated) or the auxiliary channels (activated). It is not possible to display the fNIRS and the Auxiliary data at the same time.

Sources panel

This panel is used to control the state of the light sources. By pressing the "All On/Off" you toggle the state of all sources at the same time (when activated, it makes all sources to be ON, when deactivated it turns OFF all the sources). If we instead press one of the numbers, it will toggle all wavelengths in that particular optode only (activated: all wavelengths on; deactivated: all wavelengths off). Or, by pressing one of the buttons labeled with the wavelength (in nm), that particular wavelength of the source is toggled. If the intensity level of a light source is predetermined (as in ninjaNIRS), the controls in this panel will always set the intensity of an ON source. This means that if an optode is configured as "detector only", the sources in that detector are configured with an intensity of zero; thus, their LEDs won't turn on even when pressing the button.

Detectors panel

This panel is used to control the gain of the detectors and check their saturation status (if compatible). If the detector gain is not controllable (as in ninjaNIRS, displayed), the controls for the gain control do not appear. The "Rate" control sets the sampling rate of the acquisition if it's controllable.

Stim mark: this button generates a manual stimulus mark at the time the button is pressed. Generally stim marks are best if generated automatically by the task presenting computer as an electrical signal recorded as an auxiliary channel, but the stim mark button can be used if necessary.

Start/Stop button: this button starts or stops the acquisition of the data.

Auxiliaries panel: this button is used to control which auxiliaries to display. They are color-coded according to the font color of the labels.