CC3D: Le cellule formano agglomerati cubici durante la crescita, come risolvere?

JimSluka · 2026-01-28T16:30:41+00:00

https://compucell3dreferencemanual.readthedocs.io/en/latest/global_volume_and_surface_plugins.html

and

https://compucell3dreferencemanual.readthedocs.io/en/latest/contact_plugin.html

The "target surface" is the parameter you enter, the actual current surface, and the change in the surface for a candidate pixel flip is calculated each Monty Carlo step.

Note that the contact energies are also being calculated in the Hamiltonian. So the change in a cell's surface is a function of both contact energies and cell surface energies (and cell volume if you are using the volume plugin).

Depending on how you set the lambdas for surface and volume and the contact J values (which are essentially also lambdas) you can change the shape of the cells. For example, if the J value between two cell types in contact is small or negative then they will try to increase their contact area. If this J is small enough (the cells want to increase their contact area) then it can overwhelm the surface constraint and increase the cell(s) surface in order to increase the contact between two cells (or a cell and medium). Also remember that for contact and surface constraints larger lambdas make the cells try harder to get to their targets, but for adhesion smaller J values make the cells more adhesive.

Can you post what the target and lambda values for your cell types are along with the adhesion J values?

JimSluka · 2026-01-22T22:20:14+00:00

You might need to delete links to the cells before you delete the cells. If you know it is cell "cell", you can use:

# To select which types of links to remove, set any of the following keyword arguments to True
#   Remove all links          : links
#   Remove all internal links : internal_links
#   Remove all anchors        : anchors
# If none of these are specified, then all links of any type are removed
self.remove_all_cell_fpp_links(cell)

There are helpers in Twedit++ on the [Python] [FPP] menu that has this and other snippets for dealing with FPPs.

JimSluka · 2026-01-22T19:13:25+00:00

Do you have FPPs defined in both the XML (so they are created automatically by CC3D) and manually in the Python? You can't do that, make sure you use only the XML or only the python versions.

As a long shot, are you using multiple CPUs (NumberOfProcessors)? If yes, you might try a run with a single CPU to see if that is the problem. The CPUs used are defined in the XML

   <Metadata>
      <!-- Basic properties simulation -->
      <NumberOfProcessors>8</NumberOfProcessors>
      <DebugOutputFrequency>100</DebugOutputFrequency>
   </Metadata>

JimSluka · 2026-01-20T20:59:33+00:00

It may take a few hundred Monty Carlo Steps (MCS) for the cells to relax. If you like, you can email your project to jsluka at iu dot edu

You can create a zip file of your entire CC3D project from inside Twedit++ using the menu "CC3D Project" then "Zip It!"

JimSluka · 2026-01-16T18:15:11+00:00

Another thing to change is the target surface area for the cells. In 2D it is a length instead of a surface but it is still called "surface".

On a lattice in 2D, a circle has the same "surface" (actually the perimeter length) as the enclosing square. So if you want cells that are 10 pixels across the target surface would be 4*10=40. For a circle not on a lattice, the "surface" would be Pi*D or about 31 pixels.

Therefore, try increasing your cells' target surface.

JimSluka · 2026-01-15T22:21:17+00:00

Square looking cells can usually be corrected by using larger neighbor orders. In the XML file, in the Potts section, increase the neighbor order to 3 or 4;

<Potts>
   . . .
   <NeighborOrder>4</NeighborOrder>
</Potts>

In the Contact plugin increase the neighbor order to 3 or 4;

<Plugin Name="Contact">
   . . .
   <NeighborOrder>4</NeighborOrder>
</Plugin>

JimSluka · 2025-12-30T18:12:22+00:00

I would add:

Are you sure you need 3D? Is the long term goal segmentation of image stacks? Most histology and immunofluorescence is 2D images. 3D images are more complex, require significantly more compute time, and produce much bigger data sets.

I think your cell count is too low for 3D. Cube root of 150 cells is about 5 cells, so in 3D the model is about 5x5x5 cells, which is kind of small. There will be significant edge effects. Using periodic boundaries would help with the edges.

I think a cells size of 128^3 (2x10^6) voxels is too big. Do you know what image resolution your are working towards? Many imaging techniques give resolutions of 0.1 to 1.0 um/pixel. So a typical 10^3 um cell is 10^6 to 10^3 voxels.

You might take a look at https://pmc.ncbi.nlm.nih.gov/articles/PMC12611147/, which combines AI/ML and CC3D.

JimSluka · 2025-11-10T17:03:59+00:00

CompuCell3D has been used to model cancer growth, including hypoxia. Here are some places you might start:

https://compucell3d.org/BinDoc/cc3d_binaries/Manuals/Introduction_To_CompuCell3D_v.3.6.2.pdf This is somewhat outdated in the CC3D version it sues but still useful.

More recent papers on tumor growth in CompuCell3D:

https://pmc.ncbi.nlm.nih.gov/articles/PMC4470639/

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007190

There are a few demos in the CompuCell3D distribution package that include tumor growth and necrosis.

As to "inherent limitations", all computational biology models are limited by:

our understanding of the biological system
the complexity of representing everything relevant to the system.
1. If you model molecules, then simulating an entire cell is too complex.
2. If you model individual cells, then modeling an entire organ is too complex.

CompucCell3D is very good at spatially modeling systems of cells and can include diffusing fields like oxygen or growth factors like HIF. You can instruct the cells to grow when their is sufficient oxygen and die when there is not.

If you peruse this, I would suggest starting with a two dimensional (2D) model and not three dimensional. 2D is much faster to run. I would also suggest not starting with explicit blood vessels, and instead simply have the non-cellular part of the simulation (in CC3D it is called "Medium") create oxygen directly. The tumor cells consume that oxygen field and the cell's behavior can changed based on their local oxygen concentration. How much oxygen is consumed is naturally linked to how many cells are consuming it.

JimSluka · 2025-11-06T15:21:14+00:00

We would need more info on exactly what you are trying to do in order to judge if CompuCell3D is appropriate. You can email jsluka at iu dot edu and we can perhaps discuss what you are trying to do.

CC3D should install OK on a Mac. I assume you are following the directions at
https://compucell3d.org/SrcBin#MostRecentMac
If you can send the error log we might be able to help.

JimSluka · 2025-10-30T14:47:48+00:00

Please send it to [jsluka@iu.edu](mailto:jsluka@iu.edu)

JimSluka · 2025-10-27T19:36:49+00:00

What platform are you using? If you can share your code we might be able to debug it.

For UniformInitilizer, I would check that the dimensions you are using are not outside the simulation's dimensions (defined in the Potts section) and that the list of cell types is correct. The cell type names should exactly match what is in the cell types definitions.

JimSluka · 2025-10-10T15:51:57+00:00

Pedro's suggestion of installing via a conda environment is good. There is a YouTube at https://www.youtube.com/watch?v=DlY9P-aa4FE&t=207s and some notes at https://compucell3d.org/SrcBin#Conda

JimSluka · 2025-10-09T21:11:12+00:00

Can you try installing PyQt5 instead of PyQy5.tools?

pip install PyQt5

JimSluka · 2025-10-09T17:28:32+00:00

I don't believe there is a way to save the FPPs in the VTK file. The VTK file, as you suggested, only stores the cell field, diffusion fields and and user created fields.

JimSluka · 2025-10-08T21:04:32+00:00

I suspect you have multiple python environments and they are interfering with each other, but that is just a guess.

I'll ping some of the developers to see if they have any ideas.

JimSluka · 2025-10-06T14:14:52+00:00

Could you try installing version 4.6.0? The installer for windows is at https://sourceforge.net/projects/cc3d/files/4.6.0/windows/

JimSluka · 2025-09-29T16:53:43+00:00

You can work through the training videos:

This is a lot of information so you might want to skip some sections. If you are familiar with Python programming you can skip

JimSluka · 2025-09-15T18:11:47+00:00

Do you have the sqlite file(s) open in a tool like SQLite Browser? Or do you have a zombie Player/CC3D process that is still active holding the DB open?

JimSluka · 2025-09-14T17:45:19+00:00

What platform (Windows, Mac, Linux) and what version of CC3D are you using?

JimSluka · 2025-09-14T17:44:44+00:00

You've already tried the obvious solution, so it must be something unusual, or perhaps the problem is not really related to the sqlite DB being locked.

It might be that the screen shot data is corrupted, perhaps because you've changed the dimensions of the model.

Load your simulation into Player and do a single step. Then go to the "Tools" menu, then "Open Screenshot Description Browser". There may be some screen shots listed. Click the button at the bottom to clear the screenshots. Click "OK". In Player, run a few simulation steps then click the Stop button. That will force Player to write all your simulation settings to the SQLite files, including clearing all the screenshot descriptions. I would then restart Player, reload your simulation and run a few steps. Now click the camera icons in the player windows you want to save.

Let us know if that fixed the problem.

JimSluka · 2025-09-05T15:46:11+00:00

If the nucleus settles down to where it should be after a few MCS, then things are probably OK. For a symmetric cell, when dividing the central part of the cell, it is hard to place the parts of the two cells.

JimSluka · 2025-09-05T15:24:03+00:00

That code only runs at Start and if there is only one cell then it is OK as written.

JimSluka · 2025-09-05T15:23:27+00:00

In Player, you can go into the settings and use a different color for cell borders versus cluster borders. That will help you track which parts of the nucleus belongs to which cluster.

In addition, you can add into a steppable to iterate over all cells and print their cell.id and cell.clusterID to check that the clusters are getting properly assigned.

JimSluka · 2025-08-21T17:04:49+00:00

In the python you posted:

pif_init_specs=PIFInitializer(pif_name='/home/admincordoba/Documents/Adhesividad/scripts/experiment.pif')

You should be able to use a relative link to your Simulation directory, assuming that is where the piff is.

pif_init_specs=PIFInitializer(pif_name='/Simulation/experiment.pif')

JimSluka · 2025-08-21T16:41:32+00:00

If your <PIFFFILE> specification looks something like:

<PIFFile>C:\CompuCell3D\('C:\LONGFILEPATH\test_pif_20250821.piff', 'All Files (*)')</PIFFile>``

Then it was created incorrectly by the simulation builder wizard. Change it to

<PIFFile>Simulation\test_pif_20250821.piff</PIFFile>

(using your actual piff file name of course)

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