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 dimensions of the ground truth image that will be generated (defined in pixels).
Notice that the ground truth image has the isotropic resolution!
Currently, this service allows the users to generate three different digital phantoms.
Choose the one you are interested in. The selected one will be incorporated in the final synthetic image.
Diameter of microsphere (defined in microns).
The position of each digital phantom can be either randomly generated
or defined by user.
As the simulation is longlasting process you won't be willing to spend hours
by sitting in front of your computer and waiting for the results.
Filling you e-mail here you will be notified after the process is finished,
or if it happens something important.
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 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)
Please, define the physical distance (in microns) between
each individual z-postion of the stage.
Define the efficiency of using the dynamic range of camera.
Define the shift of the generated image (VOI) with respect to the centre
of the total visible area (the whole CCD chip).
The dimensions of the final synthetic image (defined in pixels).
logo [ About this project ]
Microscope Microscope adapter Confocal unit Confocal unit adapter Objective Excitation filter Emission filter
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss 40x/1.30 Oil 488/4, Andor Laser 528/38 FITC Semrock
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss 40x/1.30 Oil 561/6, Andor Laser 617/73 Cy3 Semrock
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss 40x/1.30 Oil 405/10, Andor Laser 457/50 DAPI Semrock
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss 40x/1.30 Oil 640/6, Andor Laser 685/40 Cy5 Semrock
Leica DMRXA 1x Yokogawa CSU-10 1x Leica 100x/1.30 Oil 561/6, Andor Laser 615/60 HQ Chroma
Leica DMRXA 1x Yokogawa CSU-10 1x Leica 100x/1.30 Oil 488/4, Andor Laser 525/50 HQ Chroma
Leica DMRXA 1x Yokogawa CSU-10 1x Leica 100x/1.30 Oil 640/6, Andor Laser 700/75 HQ Chroma
Zeiss 200M 0.63x None 1x Zeiss Plan-Apochromat 100x/1.40 Oil 365 DAPI Zeiss 445/50 DAPI Zeiss
Zeiss 200M 0.63x None 1x Zeiss Plan-Apochromat 100x/1.40 Oil 640/30 Cy5 Zeiss 690/50 Cy5 Zeiss
Zeiss 200M 0.63x None 1x Zeiss Plan-Apochromat 100x/1.40 Oil 470/40 EGFP Zeiss 525/50 EGFP Zeiss
Zeiss 200M 0.63x None 1x Zeiss Plan-Apochromat 100x/1.40 Oil 550/25 Cy3 Zeiss 605/70 Cy3 Zeiss
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss Plan-Apochromat 100x/1.40 Oil 488/4, Andor Laser 528/38 FITC Semrock
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss Plan-Apochromat 100x/1.40 Oil 561/6, Andor Laser 617/73 Cy3 Semrock
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss Plan-Apochromat 100x/1.40 Oil 405/10, Andor Laser 457/50 DAPI Semrock
Zeiss 200M 1x Yokogawa CSU-10 2x Zeiss Plan-Apochromat 100x/1.40 Oil 640/6, Andor Laser 685/40 Cy5 Semrock
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss 40x/1.30 Oil 567/15 Semrock, M-G Laser 617/73 Cy3 Semrock
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss 40x/1.30 Oil 650/13 Semrock, M-G Laser 685/40 Cy5 Semrock
Leica DMRXA 1x Yokogawa CSU-10 1x Leica 100x/1.30 Oil 647/10 Chroma, Ar/Kr Laser 700/75 HQ Chroma
Leica DMRXA 1x Yokogawa CSU-10 1x Leica 100x/1.30 Oil 568/10 Chroma, Ar/Kr Laser 615/60 HQ Chroma
Leica DMRXA 1x Yokogawa CSU-10 1x Leica 100x/1.30 Oil 488/10 Chroma, Ar/Kr Laser 525/50 HQ Chroma
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss Plan-Apochromat 100x/1.40 Oil 488/4, Andor Laser 528/38 FITC Semrock
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss Plan-Apochromat 100x/1.40 Oil 561/6, Andor Laser 617/73 Cy3 Semrock
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss Plan-Apochromat 100x/1.40 Oil 640/6, Andor Laser 685/40 Cy5 Semrock
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss 100x/1.45 Oil 488/4, Andor Laser 528/38 FITC Semrock
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss 100x/1.45 Oil 561/6, Andor Laser 617/73 Cy3 Semrock
Zeiss S100 1x Atto CARV 1x Zeiss 63x/1.40 Oil DIC (new) 555/28 Cy3 Chroma 617/73 Cy3 Chroma
Zeiss S100 1x Atto CARV 1x Zeiss 63x/1.40 Oil DIC (new) 490/20 FITC Chroma 528/38 FITC Chroma
Zeiss S100 1x None 1x Zeiss 63x/1.40 Oil DIC (new) 403/12 DAPI Chroma 457/50 DAPI Chroma
Zeiss S100 1x Atto CARV 1x Zeiss 63x/1.40 Oil DIC (new) 635/20 Cy5 Chroma 685/40 Cy5 Chroma
Zeiss S100 1x None 1x Zeiss 63x/1.40 Oil DIC (new) 555/28 Cy3 Chroma 617/73 Cy3 Chroma
Zeiss S100 1x None 1x Zeiss 63x/1.40 Oil DIC (new) 490/20 FITC Chroma 528/38 FITC Chroma
Zeiss S100 1x Atto CARV 1x Zeiss 63x/1.40 Oil DIC (new) 403/12 DAPI Chroma 457/50 DAPI Chroma
Zeiss S100 1x None 1x Zeiss 63x/1.40 Oil DIC (new) 635/20 Cy5 Chroma 685/40 Cy5 Chroma
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss 100x/1.45 Oil 650/13 Semrock, M-G Laser 685/40 Cy5 Semrock
Zeiss 200M 0.63x None 1x Zeiss 100x/1.45 Oil 640/30 Cy5 Zeiss 690/50 Cy5 Zeiss
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss 100x/1.45 Oil 488/6 Semrock, M-G Laser 528/38 FITC Semrock
Zeiss 200M 0.63x None 1x Zeiss 100x/1.45 Oil 470/40 EGFP Zeiss 525/50 EGFP Zeiss
Zeiss 200M 1x Yokogawa CSU-10 1x Zeiss 100x/1.45 Oil 567/15 Semrock, M-G Laser 617/73 Cy3 Semrock
Zeiss 200M 0.63x None 1x Zeiss 100x/1.45 Oil 550/25 Cy3 Zeiss 605/70 Cy3 Zeiss
Zeiss 200M 0.63x None 1x Zeiss 100x/1.45 Oil 365 DAPI Zeiss 445/50 DAPI Zeiss
Not available

volume_info x x microns
fullframe_info
precision_info
pixel_info Ground truth volume x x voxels

Phantom
phantom_info
diameter_info microns
position_mode_info Position:
amount_random_info

set_info
objective_info
excitation_filters_info
emission_filters_info
camera_info
time_info milliseconds
z_step_info microns
usage_info %
shift_info
final_pixel_info Final volume x x voxels
email_info