Randy Heiland

SVG image plot on studio results in a plot with X = Y = (0, 1)

Terrific - thanks for letting us know. I'll close the ticket.

Hello, If you're willing to share your model (your .xml) and perhaps your snapshot00000000.svg, it may be helpful. If you'd rather keep it private, send via email (heiland@iu.edu). So far, I'm unable to reproduce the problem. What should happen is the Studio ignores the substrate info in the .svg and uses the .mat data to plot substrates. Therefore you do need to save the "Full" data (Config Basics tab).

Can you say more about how you'd like to change the initial cell positions? As you've probably learned, they are currently done in the setup_tissue() in the custom_modules/cancer_immune_3D.cpp. And it calls create_cell_sphere_positions which creates the cells' positions.

For starters try running that model with the full output flag to false. Just save the SVG. On Wed, Jan 10, 2024 at 9:06 AM Steven S ssummey@users.sourceforge.net wrote: g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 I ran the heterogeneity-sample project as well and it ran smoothly. I realize the simulation from the literature had several custom modules and adjusted settings for their model; however, when running that simulation, I noticed the output file sizes were considerably large for the time-steps...

Let's start with something simpler. Can you provide your terminal output when compiling and trying to run the "template" project, i.e., these commands: make reset make template make project You might also provide "g++ --version"

This is quite specialized. Do you have a model that doesn't require Boost?

Check out Furkan's presentation from last summer's workshop: https://github.com/physicell-training/ws2023/blob/main/agenda.md#advanced-session-4-intracellular-with-libroadrunner-introduction If you've downloaded PhysiCell, you could try building/running the ode-energy-sample: (base) M1P~/dev/PhysiCell_V1.13.1$ make ode-energy-sample ... You may need to step through the PhysiCell setup slides also linked on the above agenda, if you haven't yet.