Configuration that has been used for calculating

;

;--------------- characteristics of one 'universal' cell ----------------

;

[cell]

; Should be 46 for humans.

chromosome count = 46

; Lengths of phases of cell cycle

; (in percents)

;

; Well, they sum up to only 95% (not 100%) and that is because

; there is Cell::SetDelay() executed after cytokinesis, which

; delays, that is, lengthen/enlarges, the budget of the G1 phase

; by 0% to 10%  (with mean of 5%) of the cell cycle length.

; So the \e durationOfG1Phase ranges, in fact, from 45% to 55%

; yielding new total of 95% to 105% (with mean at 100%).

;

; times correspond to literature

duration of G1 phase = 45.0

duration of S phase = 30.0

duration of G2 phase = 15.0

duration of prophase = 1.25

duration of metaphase = 2.85

duration of anaphase = 0.25

duration of telophase = 0.325

duration of cytokinesis = 0.325

;

;testing:

;durationOfG1Phase = 1.0

;durationOfSPhase = 1.0

;durationOfG2Phase = 1.0

;durationOfProphase = 1.0

;durationOfMetaphase = 1.0

;durationOfAnaphase = 1.0

;durationOfTelophase = 20.0

;durationOfCytokinesis = 1.0

;

;

; amount of fluorophore molecules filling the nucleus interior

; (in percents)

;

coverage = 300.0

;

; The average diameter of standard cell (in microns)

;

cell diameter = 7.0

;

; A diameter of nucleolus (in microns)

;

nucleolus diameter = 1.4

;

; How far a cell can normally move between frames (in microns)

;

; When setting this value, take into account how many

; frames are used to sample cell cycle, which correlates

; with time delay between acquisition of frames in real

; situation

;

; Default value is based on our observation that a cell

; moves 1.5-2.0um/frame if time-sampling is 9.5min/frame,

; and about 1um/frame if time-sampling is 5min/frame. Thus,

; both cases yield "average" velocities of 0.184um/min and 0.2um/min.

; We use 0.19um/min and 23.75hrs/cycle.

;

; This value must not be greater than cellLookDistance.

;

; Erik data:

; cellMagnitudeOfMovementPerFrame = 0.6 

;

; short sequences

cell magnitude of movement per frame = 1.4

;

; How far a cell can move between frames (in microns) if the cell is cometing.

; Refer to the type StateOfComet for details about cometing.

;

comet cell magnitude of movement per frame = 0.5

;

; maximum magnitude of vectors used for usual and occuring-most-of-the-time

; non-rigid deformation of cells (in microns)

;

; short sequence:

cell nonrigid deformation = 0.15

;

; maximum magnitude of vectors used for "strong" non-rigid

; deformation of cells (in microns); this deformation typically

; happens just occasionally and, unlike the deformations driven

; with the cellNonRigidDeformation constant, one usually notices it;

; if set to zero, the "strong" deformation is disabled

;

; observed from Erik's data:

; cellNonRigidStrongDeformation = 1.0

;

; short sequence:

cell nonrigid strong deformation = 0.7

;

; Should or shouldn't non-rigid deformations (if available) be done

; in every frame. It is good to disable them when noFramesPerCellCycle

; is more than 60.

;

; Erik's data:

; const bool cellSparseNonRigidDeformations=true;

;

; short sequences:

cell sparse nonrigid deformations = false

;

; How far a cell can "see" when it is trying to move

; to region with lower density of cells (in microns).

;

; The higher the value is, the greater outlook a cell has

; and the higher chance it flows into less dense region (

; and the higher time demand for the simulation :-).

;

; This value must not be less than cellMagnitudeOfMovementPerFrame.

;

; Erik data:

; cellLookDistance = 1.1f*cellMagnitudeOfMovementPerFrame; 

;

; short sequences:

cell look distance = 6.0

; two presets available: "Erik data" vs. "short sequences"

;

; Default (average) number of frames per cell cycle

;

; Observation: 

; 150 frames/cycle gives 9.5min/frame provided cycle lasts 23.75 hours.

; 285 frames/cycle gives 5min/frame provided cycle lasts 23.75 hours.

;

; Erik data:

; noFramesPerCellCycle = 150

; short sequences:

number of frames per cell cycle = 100

; Eva data:

; noFramesPerCellCycle = 280; 

;

;-------------- characteristics of scheduler -------------------

;

[scheduler]

;

; Number of initial cells put into the process

;

number of initial cells = 10

;

; A constant that defines which slice from fully _ISOtropic_ 3D image

; should be used for spatiotemporal image. The spatiotemporal images

; are created from the ISOtropic images before these are anisotropically

; resampled.

;

slice of interest = 60

;

;---------------- optical system --------------------------------------

;

;

[objective]

name = Zeiss 63x/1.40 Oil DIC (new)

magnification = 63

[microscope]

name = Zeiss S100

magnification = 0.859

[microscope adapter]

magnification = 1

[confocal unit]

name = Atto CARV

magnification = 1

[confocal unit adapter]

magnification = 1

[psf]

;experimentaly measured point spread function

;corresponding to the selected components

;location = /mnt/gryf/COMMON/DATA/PSF/2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

location = 2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

;location = /home/xulman/gryfCOMMON/DATA/PSF/2013-01-30_1_1_9_0_2_0_0_1_0_0_0_0_11_14.ics

[light source]

;experimentaly measured quadratic surface of uneven illumination

;corresponding to the selected components

b1 = 0.8507717563

b2 = 0.0003232258

b3 = 0.0002796816

b4 = -0.0000000193

b5 = -0.0000003282

b6 = -0.0000002623

[fluorophore]

photobleaching rate = 0.003

[camera]

name = Micromax 1300-YHS

pixel size = 6.7

dynamic range = 12

grid = (1300,1030)

baseline = 550

ADC gain = 6

ADC offset = 0

read out noise = 25

dark current = 0.1

full well depth = 18000

[acquisition]

time = 5000

dynamic range usage = 85

[table]

z step = 0.2

[voi]

; size and shift in microns

size = (86.7,86.7,9.3)

shift = (0,0)

[subpixel precision]

level = 1

;

;--------------- testing mode options ----------------

;

[testing]

;

; When starting the simulation with the '-g' parameter (use given initial

; masks image/file), the following two integer parameters override the span

; of IDs which the simulator searches for. Note that the created cells will

; receive their own IDs, independently of the mask image.

;

; Used in the Scheduler constructor. Should be positive natural numbers.

init mask min label = 7

init mask max label = 11

;

; For non-rigid deformations, the simulator uses a coherent deformation pool

; saved as the Scheduler::pnArray. At the start up, if this data is not found

; in a cache file pnArray.cache on harddisk, a new one is automatically

; created. When creating the new one, its 3D+t size is typically derived from

; the cell diameter (times a factor of 3.5x times scene resolution) and from

; the Scheduler::GetInterphaseBudget(). With this option, one can override

; the default. Typically we want to make it a lot tighter...

;

; Used in the main() function. The factor is a positive real number,

; the length is positive natural one.

;pnArray xyz factor = 2.0

;pnArray z length = 52

;

; The simulator is capable of performing 'strong non-rigid deformations'

; occasionally. The average number of frames between two consecutive

; 'strong deformations' is normally inferred the duration of the G2 cell

; cycle phase. This parameter may override this average delay [in frames].

;

; Used in the Cell constructor and Cell::ScmSuggestNonrigidDeformation().

; Should be positive natural number.

;strong deformation delay = 10

;

; This option overrides the simulation scenario (whatever is currently used,

; e.g., interviewing Scheduler::Run(...) with creation of comets) by calling

; a single Run(X) with X read from this parameter.

;

; Used in the main() function. Should be positive natural number.

;single run length = 1

;

; When starting the simulation, every cell starts initially in the G2 cell

; cycle phase and stays there for some random time. This parameter overrides

; this random time and, actually, fixes it for all cells to the same specified

; value.

;

; Used in both Scheduler constructors. Should be positive natural number.

cell initial G2 life = 5

;

; If rigid movement of cells is enabled in the CMake, this parameter can

; disable it. It cannot, however, enable it if the rigid movement is disabled

; in the CMake (as the code is simply missing in the simulator binary then).

;

; Presence of the parameter with any value disables the movements,

; and vice versa.

;disable rigid movement = 1

; If this parameter is present, the routine for rendering territories into

; images will render the nucleus boundary as the very first thing.

;territories with nucleus boundary = 1

; If this parameter is present, the routine for rendering territories into

; images will not render all chromatin but, instead, only the chromatin

; which is listed in the parameter.

;

; Note that the number of chromatin present in the simulation is defined

; in the [cell] section of this configuration file. So, the numbers listed

; in this parameter should range from 0 up to (the number of chromatin minus 1).

;territories show only these chromatins = 15 30 45

// The frequency of restarting the chromatin (texture)

// note: set high number to disable it

#ifndef GTGEN_WITH_SOFA

	#define RESTART_PERIOD 4

#else

//#ifndef GTGEN_WITH_SOFA

	//#define RESTART_PERIOD 4

//#else

	#define RESTART_PERIOD 1000

#endif

//#endif

/**

 * A helper function to provide IDs for objects which guarantees their uniqueness

			  			// The noFramesPerCellCycle should slightly vary between cells to simulate

			  			//  non-uniformity of cells in population.

						cellCycleLength = (size_t) floorf(GetRandomGauss(cellCycleLength, 

																						 0.05f*cellCycleLength));

																						 0.17f*cellCycleLength));

						REPORT("new cell has cycle length " << cellCycleLength << " frames");

					}

template <class MV, class PV>

void Cell<MV, PV>::ChrReportStats(void)

{

	/*

	for (size_t i=0; i < chrCentres.size(); ++i)

	{

		DEBUG_REPORT("chromosome " << i << " has centre coordinate "

			<< chrCentres[i].pos << " um, spread of "

			<< chrSpreads[i] << " um, and density " << chrDensities[i]);

	}

	*/

}

//-----------------------------------------------------------------------------

template <class MV, class PV>

void Cell<MV, PV>::ChrReportClosests(void)

{

	/*

	for (size_t i=0; i < chrCentres.size(); ++i)

	{

		float closests_dist=100;

		DEBUG_REPORT("chromosome " << i << " has closest chromosome "

			<< closests_ID << " at distance " << closests_dist << " um");

	}

	*/

}

#endif

		if (availTrans >= 5) {

			//make cellMagnitudeOfMovementPerFrame vector lengths the most popular

			MultiplyWithRadialGaussian(mm,cellMagnitudeOfMovementPerFrame,cellLookDistance/3.f);

			//MultiplyWithRadialGaussian(mm,cellMagnitudeOfMovementPerFrame,cellLookDistance/3.f);

			MultiplyWithRadialGaussian(mm,cellMagnitudeOfMovementPerFrame,1.33f*cellMagnitudeOfMovementPerFrame); //=4/3*vel

			//

			//mm.SaveImage("MovsMask-radial.ics");