VIOLA User Manual
VIOLA is a tool to visualize neuronal activity data in multiple 2D layers in an
interactive and efficient way.
Assuming that you started VIOLA in a browser
(Google Chrome preferred) as described in the
README,
this User Manual introduces the main panels for Configuration,
File upload, and the various
Visualization components, which offer different
perspectives on the data to be analyzed.
There is a Control bar to steer the tool and
Keyboard shortcuts facilitate to control 3D views.
Upon startup, VIOLA opens the Setup Page to configure the visualization for a specific data set.
The setup panel offers input fields for the specification of meta information
regarding the data to be analyzed and the initialization of the visualization.
You may either load an existing configuration file (with extension .json, see
README) or enter the
parameters manually.
Default values correspond to the example data in
PreprocessedData.zip.
The available parameters for the data to be visualized depend on the data type
(raw or preprocessed).
Preprocessed Spike data can be visualized simultaneously with an
Analog signal like the LFP.
The bottom segment Display offers configuration options for the visual
representation.
Having entered all parameters, click the button Setup visualization to get to the Main Page.
Using the Upload Panel to the left of the Main page, you can upload all
files for the data to be visualized corresponding to the file names specified in
the Setup panel:
either by dragging and dropping the files to the blue box or by opening a file
explorer with the corresponding button.
If the background color of the field for a data file changes from red to green,
the upload has been successful.
As soon as all files are uploaded, close the upload panel by clicking the x
at its top right corner.
You can drag the blue cursor to navigate through time, or use the buttons to
start (Play) or stop (Pause) the automatic animation.
Clicking < or > moves to the previous or next visualization step,
respectively.
With << and >>, you can switch between running the animation backwards
or forewards, respectively.
Pressing the Reset button resets the position of the camera in case of the
3D views, and goes back to the first time step of the data.
We here introduce the visualization concepts with the example of preprocessed
data.
Views 1 and 2 show instantaneous snapshots of data in space, while views 3 and 4
show time series of data.
The visualization can be customized with the menu bar and different interactive
controls in the respective visualization panels.
The panel displays the number of spikes per second occurring in a spatiotemporal bin; one square layer per neuron population.
Population layers from view 1 are stacked such that different populations are on
top of each other.
The size of the cubic markers represents the instantaneous spike count of the
spatiotemporal bins.
Projections of the spike counts are shown towards the edges.
The panel shows a time-series representation around the present time step
(vertical white line).
The black curve indicates the total instantaneous spike-count rate summed over
all populations, and the stacked, normalized histogram shows the relative
fraction per population of the total of spike count.
Activate the 3D timeline in the menu bar: 3D View -> Scene -> 3D Timeline.
In this timeline representation, spike-count rates are resolved in time and
space.
The spike count is rendered as closed iso-value surface.
A time lag of zero corresponds to the present time step.
[Space]: Play/pause the simulation.
[Shift] + [S]: Switch between 3D Timeline and Layer scenes
[Shift] + [C]: Switch between fixed and free camera
[Shift] + [L]: Switch between AZERTY and QWERTZ/QWERTY layouts
[Shift] + [M]: Switch camera mode between Orthographic and Perspective
Use W, A, S, D (resp. Z, Q, S, D in AZERTY layout) to rotate the camera around the center.
Use Q (resp. A) and E to zoom in/out.
Use [Up] and [Down] arrows to decrease/increase the distance between the center and the camera.
Use W, A, S, D, R, F (resp. Z, Q, S, D, R, F) to move the camera.
Use Q (resp. A) and E to zoom in/out.
Use [Up], [Down], [Left] and [Right] arrow to rotate the camera.