https://doi.org/10.5061/dryad.dz08kps5v

'CellTrajectoryVer2':
This research focuses on computer simulations of cell dynamics, including cell division, differentiation, apoptosis, and movement in three-dimensional (3D) space, using the 'Biosim' code. The output file "mark.dat" from 'Biosim' contains cell coordinates in 3D space, cell lineage denoted as MK.ID, and cell positions (PREPOS) at time t-1, a one-time step before, for all cells at each time point t during the simulation. This output file was used as input for our custom software 'CellTrajectoryVer2' to reconstruct cell trajectories.

Description of the data and file structure

Installation and Setup:

1. Installation:

• Double-click the 'CellTrajectoryVer2.exe' repository to install the necessary files, including 'CellTrajectory.exe.'
• The necessary files are installed in the folder C:\Cell.

1. Running 'CellTrajectory':

• Double-click 'CellTrajectory.exe' in the folder C:\Cell to open the software.
• The software comprises two sequential processes for assigning input information:　‘Prepare in advance’ and ‘Creation of cell trajectory data’.

Process Steps:

1. Prepare in Advance (Figure 1, left):

• Pre-process 'mark.dat' to classify data by MK.ID for cell lineage.
• Enter the path to 'mark.dat' and specify the folder for the output files.
• Output files ‘mark*.dat’ are generated, named mark1.dat, mark2.dat, etc., for normal cell lineage, and mark20001.dat, mark20002.dat, etc., for leukemic cell lineage.
• Press the ‘execute’ button.

1. Creation of Cell Trajectory Data (Figure 1, right):

• Reconstruct all cell trajectories during the simulation based on PREPOS.
• Select a target cell from all cells existing at an arbitrary ending time point (t_end) and assign the coordinates (x, y, z) of the target cell, the focused MK.ID, t_end, and the starting time point (t_start).
• Specify the corresponding mark*.dat file and the name of an output file.
• Press the 'extract the target data' button.
• Press the 'create the trajectory data' button and assign the name of the final output file, which will include data for all cell trajectories.

Source Codes:

• The source codes for cell trajectory reconstruction in ‘CellTrajectory.exe’ are ‘MainForm.cs’ and ‘PointXYZ.cs.’

Visualization:

• Cell trajectories in 3D space were visualized using Origin 2022 (OriginLab).
• An interface, 'cellgraph_v5_2021b.opx,' was developed to facilitate the transfer of trajectory data from the final output file of 'CellTrajectoryVer2' to Origin 2022.
• To use this interface, import 'cellgraph_v5_2021b.opx' into the opened Origin window by dragging and dropping it. Once imported, the final output file can be imported into Origin, allowing for the representation of cell trajectories in 3D space.

Sharing/Access information

NA