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CompuCell3D 4.9.0

Release date: May 16 2026

We are excited to announce that binaries and conda packages for CompuCell3D v4.9.0 are now available! This release focuses on portable simulation-specific settings, improved Player state restoration, better DeveloperZone workflows, and updates to Twedit++ code generation and simulation authoring tools.

🌟 What's New in v4.9.0

Here are the highlights:

1. Portable Simulation Settings

CompuCell3D now has a more complete workflow for saving and reusing visualization and Player settings:

  • Simulation-Specific Settings Simulations can now load custom XML settings from Simulation/_custom_settings.xml.

  • Settings Export Player settings can be exported to XML, making it easier to share visualization preferences with a simulation.

  • Settings Management Dialog The Player includes a new Manage Simulation Settings dialog for exporting and deleting simulation-specific settings.

  • Python and Notebook Workflows XML-based and SQLite-based custom settings are supported in Python-only simulations using CC3DPy.py, and custom XML settings are supported in notebook workflows.

  • Alternate Global Settings Directory A new --global-settings-dir-name command-line option allows users to select an alternate global settings directory name under the user home directory.

2. Player Usability & Visualization Improvements

  • Faster Settings Access An in-memory settings cache improves settings access performance and defers disk writes while simulations are running.

  • Improved Window Layout Restoration Player dock window sizes, startup position, and XML-serializable window layout settings are restored more reliably.

  • Better Non-MDI Layout Behavior Model Editor, Cell Type Colors, and Console dock windows are easier to resize in non-MDI layouts.

  • Improved Color Handling Settings color specifications now accept HTML color names such as orange, magenta, and darkblue.

  • Clearer Status Reporting Simulation settings and movie generation dialogs now use clearer in-dialog status messages.

3. Core, XML & Headless Workflow Updates

  • Improved Settings Propagation Custom visualization settings are propagated more reliably from the main process to child processes, improving headless and multiprocess workflows.

  • Headless Screenshot Fixes Screenshots generated by run_script.py now update correctly, and 2D screenshots use the correct custom colors across subsequent captures.

  • Extended XML Schema Support XML schema validation now allows extended attributes on Plugin, Steppable, CompuCell3D, and Metadata elements.

  • Improved Export Formatting Exported settings XML is formatted more cleanly, with clearer messages about written SQLite and XML settings files.

4. Twedit++ & Developer Tools

  • New Simulation Wizard Dialogs Twedit++ adds wizard dialogs for the Contact and ContactInternal energy plugins.

  • Improved Generated C++ CMake Files CMakeLists.txt generation for C++ plugin code created by the Twedit++ C++ helper has been improved and corrected.

  • Improved Python Helper Snippets The Python helper snippet for opening files from generated code has been improved.

  • DeveloperZone Improvements DeveloperZone configuration and build support were fixed and improved, including better CMake install normalization.

🛠 Bug Fixes & Improvements

  • Fixed non-updating screenshots in headless run_script.py workflows.
  • Fixed 2D screenshot coloring so subsequent screenshots use the correct custom colors.
  • Fixed Player startup position and dock window size restoration from saved settings.
  • Fixed hard-to-resize dock widgets in non-MDI layout.
  • Fixed crash when creating a second FocalPointPlasticity anchor.
  • Fixed generated plugin CMakeLists.txt content from the Twedit++ C++ plugin helper.
  • Fixed commenting out of XML snippets that already contain comments.
  • Fixed Parameter Scan.
  • Fixed macOS x86-only version metadata.
  • Updated version metadata to 4.9.0 across the suite.
  • Multiple minor cleanup and stability fixes.

🚀 How to Install

Option 1: Binary Downloads

👉 Download CompuCell3D v4.9.0 Binaries

🪟 Windows

If CC3D fails after upgrade: - Remove old installation directory - Remove _settings.sqlite if needed

🍎 macOS

Before installing:

rm -rf ~/CompuCell3D

Apple Silicon (M1/M2/M3)

Download: cc3d-installer-osx-4.9.0-arm64.sh

chmod +x cc3d-installer-osx-4.9.0-arm64.sh
./cc3d-installer-osx-4.9.0-arm64.sh

To run:

cd ~/CompuCell3D
./compucell3d.command

Intel Macs

Download: cc3d-installer-osx-4.9.0-x86.sh

chmod +x cc3d-installer-osx-4.9.0-x86.sh
./cc3d-installer-osx-4.9.0-x86.sh

🐧 Linux

Before installing:

rm -rf ~/CompuCell3D

Download: cc3d-installer-linux-4.9.0-x86-64bit.sh

chmod +x cc3d-installer-linux-4.9.0-x86-64bit.sh
./cc3d-installer-linux-4.9.0-x86-64bit.sh

Install location: ~/CompuCell3D

To run:

cd ~/CompuCell3D
./compucell3d.sh

Option 2: Conda / Mamba

🔹 Quick install (existing environment)

mamba install -c compucell3d -c conda-forge compucell3d=4.9.0

Launch Player:

python -m cc3d.player5

conda create -n cc3d_490 python=3.12 -c conda-forge
conda activate cc3d_490
conda install -c conda-forge mamba
mamba install -c conda-forge -c compucell3d compucell3d=4.9.0

👉 On Windows, you may also run:

set PYTHONIOENCODING=utf-8

⚠️ Notes

  • Use conda-forge + compucell3d channels only
  • Avoid main channel to prevent conflicts
  • mamba is strongly recommended

▶️ Running CompuCell3D

Player:

python -m cc3d.player5

Twedit++:

python -m cc3d.twedit5

Headless:

python -m cc3d.run_script

📦 Optional: Install Demos

Download from: Demos

Place in: ~/CompuCell3D/Demos