Hello everyone. I simulate the migration of a cell over a substrate and I would like to obtain the velocity of this cell and the time of each iteration. Do you know if there is a way to know them? Thank you!
You can find a velocity measure by tracking positions of center of masses of cells and the time taken to attain the difference. So if the center of mass of the cell has shifted from x1 to x2 in t mcs, the velocity would be (x2-x1)/t
One thing to remember though is to be aware that is t=1 MCS (Monte Carlo Step) you will get a very noisy estimate of the velocity so it is best to use longer time periods. the optimal interval to use may depend of the actual simulation you run so you may need to play a bit with different values
Thank you for the answer. Do you know where I can find data such as the position of the center of mass of the cell during the simulation (because I try to use the plugin "CenterOfMass" but I can't find the data for post-processing)?
If you use twedit++ there is a code snipet at <CC3D Python><Cell Attributes><Center of Mass>, which inserts the code below. # Make sure CenterOfMass plugin is loaded # READ ONLY ACCESS xCOM=cell.xCOM yCOM=cell.yCOM zCOM=cell.zCOM
This is a little embarrassing, but I have used a ruler on screenshots taken at simulation start and end points to measure # of pixels/voxels traveled by a clump of cells to get their tissue-invasive velocity. The simulation was of several hours' movement, so this was basically a long, running average, as mentioned above. Whether I did it on the screen or printed on paper I can't remember, but either is fine -- though you have a record if you keep the paper. The traveling cells stayed visible in one plane of a 3-D sim, coincidentally. Not to discourage tracking it computationally -- you could just as easily get a start and end point and do the same calculation -- just another way it has been done.