After experiencing multiple Python–NEURON compatibility issues, the most reliable way to run BrainCell on Windows 11 is to perform a clean installation of both Anaconda and NEURON using mutually compatible versions.
Step 1: Clean the system
Before installing anything:
Uninstall all previous versions of NEURON and Anaconda
Remove old Python and NEURON entries from the PATH environment variable:
Open “Edit the system environment variables”
Click Environment Variables
In both User and System variables, edit PATH
Delete all entries related to Python, Anaconda, or NEURON
Restart Windows
This step is essential to avoid conflicts between different Python versions.
Step 2: Install Anaconda
Download and install:
Anaconda 2023.09 (Windows, x64)
https://neuroalgebra.net/assets/Anacond ... x86_64.exeInstallation notes:
Enable “Add Anaconda to PATH” during installation
Use default installation options
Restart Windows after installation
Step 3: Install NEURON
Download and install:
NEURON 8.2.2 (Windows, mingw, Python 3.7–3.11)
https://neuroalgebra.net/assets/nrn-8.2 ... -setup.exeThis installer includes Python interfaces compatible with Python 3.7–3.11, ensuring correct integration with Anaconda.
Step 4: Prepare BrainCell
Compile the required MOD files
Verify that NEURON starts without errors
Step 5: Run BrainCell
BrainCell can now be launched normally, for example via:
init.hoc
init.bat
No additional Python flags (-pyexe, -pylib) should be required.
Summary
A clean installation of:
Anaconda 2023.09
NEURON 8.2.2 (Python 3.7–3.11 support)
provides a stable and reproducible setup for running BrainCell on Windows 11.