Saving cell data in text files (Save cells data)

If the option icon_option Save cells data is enabled, then after the simulation is completed, in the results directory you will have a folder called Cells.

This folder contains text files called Cells_[model time]. The model time value indicated in the name indicates how many time units after the start of the simulation this text file was generated.

The number of text files will depend on the values ​​of the Max Time and Image interval parameters (see example below).

Example
Image interval = 20 (text files are saved every 20 model time units).
Max Time = 100 (simulation lasts for 100 model time units).

Text files in the Cells folder:
- Cells_0000,
- Cells_0020,
- Cells_0040,
- Cells_0060,
- Cells_0080,
- Cells_0100.

These text files provide the following data for each cell in the model:

  • X: cell coordinate along the X axis,

  • Y: cell coordinate along the Y axis,

  • Z: cell coordinate along the Z axis,

  • Radius: cell radius,

  • r: cell nucleus radius,

  • Color1: the color with which the internal contents of the cell are drawn,

  • Color2: the color used to draw the cell border,

  • Color3: the color with which the internal contents of the cell nucleus are drawn,

  • Color4: the color used to draw the border of the cell nucleus.

Note

All colors are presented in RGB format.

Note

If the text file contains only Color1 value, then it is considered that:

  • the nucleus of the cell is not drawn,

  • the cell border is drawn in black [0,0,0],

  • all internal contents of the cell are drawn with Color1.

If the text file contains only Color1 and Color2 values ​​, then it is considered that:

  • the nucleus of the cell is not drawn,

  • the border of the cell is drawn with Color2,

  • all internal contents of the cell are drawn with Color1.

An example of such a text file is presented below:

Example text file
X       Y        Z     Radius r     Color1        Color2        Color3        Color4
410.4   -26.7    0.0   8.4    5.0   [128,128,128]
-298.1  95.8     0.0   8.4    5.0   [128,128,128]
280.3   -119.7   0.0   8.4    5.0   [128,128,128]
179.5   248.1    0.0   8.4    5.0   [128,128,128]
500.1   -160.7   0.0   8.4    5.0   [128,128,128]
320.6   256.4    0.0   8.4    5.0   [128,128,128]
9.2     481.9    0.0   8.4    5.0   [128,128,128]
426.3   -212.8   0.0   8.4    5.0   [128,128,128]
41.0    65.2     0.0   8.4    5.0   [128,128,128]
-104.0  82.0     0.0   8.4    5.0   [128,128,128]