The dimensions of the volume where the objects should be generated into (defined in microns).
If highlighted in red color, the entered values are out of the range.
Remark, that setting the values drives the context of "Final volume" input field.
The following should be fulfilled: 'x' and 'y' dimensions should be less or equal
than the dimensions of selected CCD chip. 'z' depth should be less or equal to 20 microns.

The ground truth image can be oversampled to higher resolution.
Selecting "1x" corresponds to the same resolution of the ground truth
and the final image. If you choose "2x", the ground truth image dimension
will be doubled, i.e. for 3D data the volume becomes 8x higher.

Checking this box sets the width and the height of VOI to the size of chip
of selected CCD camera.

The resolution of the ground truth image that will be generated.
Notice that the ground truth image is isotropic!

The dimensions of the ground truth image that will be generated (defined in pixels).
Notice that the ground truth image has the isotropic resolution!

Please choose the digital phantom you are interested in.

As the simulation is often a longlasting process, you are not required to
have the page open in your browser during the whole process. By filling your
e-mail here, we can notify you after the process is finished.

Estimated time to complete the simulation with chosen parameters.

Note: The needed amount of time can be reduced by scaling down
the ground truth volume, by lowering the number of frames
of the time-lapse sequence, or by reducing the number of cells
on the phantom.

Select the type of point spread function (PSF) that will be used
to simulate the optical system. The experimental PSFs were acquired
using the real optical systems, whereas the theoretical PSFs are
synthetic.

Select the theoretical PSF that will be used for this simulation.

Select the virtual set (microscope and its adapter + eventually confocal unit and its adapter)
you would like to use for this simulation.

Hide set details.

Show set details.

Select the (virtual) objective you would like to use for this simulation.

Select the (virtual) excitation filter you would
like to use for this simulation.

Select the (virtual) emission filter you would
like to use for this simulation.

How much is the light source (mercury lamp, laser) axis deflected
away from the optical axis? (in microns)

Select the (virtual) camera you would like to use for this simulation.

Hide camera details.

Show camera details.

How long should the acquistion process last? (in miliseconds)
(Affects the amount of noise in the image.)

Please, define the physical distance (in microns) between
each individual z-position of the stage.
(Affects the final image resolution in z axis.)

Define the efficiency of using the dynamic range of camera.
(Affects the amount of noise in the image.)

Define the shift of the generated image (VOI) with respect to the centre
of the total visible area (the whole CCD chip).

The resolution of the final synthetic image.

The dimensions of the final synthetic image (defined in pixels).

Note: If the volume is displayed in red color, the resolution of camera
has been exceeded. In this case please choose another configuration of
virtual set, objective, and camera.

Benchmarking mode, if selected, allows to select multiple configurations
of acquisition time and stage z-step at once.

Total number configurations is 'number of steps of the acquisition time'
times 'number of steps of the stage z-step'. Configurations and final
images are indexed from 000.

List of selected configurations (acquisition time, stage z-step).
Configuration with mean values is in black color.

Hide list of selected configurations.

Show list of selected configurations.

Diameter of microsphere (defined in microns).

The position of each digital phantom can be either randomly generated
or defined by user.

If the "Random" option is chosen above the user is allowed to define the amount of the generated digital phantoms.
The upper limit (due to memory capacity) of generated object is limited by the number 10.

When the "Fixed" option is chosen baove the user is not allowed to change the amount of generated objects (digital phantoms).
The only possible value is "1". If you want to generate more than one object please, click to the button "Add new phantom" below.

You have selected "Fixed position" for the generated object.
Hence you are required to define its position (in microns).

Select the number of spots in the C. elegans phantom.

Number of cells in the initial population.

Default (average) number of frames per cell cycle.

Duration of simulated time-lapse sequence in frames.
The simulator may generate a little more frames, due to its inner achitecture.

Border width around the specimen given in percents.

Set the parameters to specific cell phenotype.

The initial number of filopodia.

Resulting duration of the experiment.
Depends on timestep and chosen number of frames of the time-lapse sequence.

The duration of global timestep in seconds
(i.e. the time between two consecutive frames).

Duration of simulated time-lapse sequence in frames.

The probability of the filopodia branching.

The probability of the appearence of the new filopodia.

the probability of the disappearence of the new filopodia.

The radius of filopodium base.

The filament depolymerization rate.

The filament base polymerization rate.

The thermal energy.

The initial length of the filaments.

The total membrane force.

The velocity of the retrograde flow.

The modulus of force vector applied to each filopodium tip
(the force direction is randomized).

The magnitude of pressures applied to cell body surface.

The coarseness of Perlin noise in cell interior. Affects granularity of the texture.

Multiplicity of how many dots should be generated between two voxel positions in filopodia.

Multiplicity of how many dots should be generated between two voxel positions in filopodia.