Quick Start: Identify Your Category
Choose the category that matches your current system:
Category Description When to Use
Category 1 NEURON + Python already working You run NEURON simulations regularly
Category 2 Clean system (nothing installed) Fresh OS or new to NEURON
Category 3 Mixed/incomplete installation
NEURON or Python partially installed CRITICAL: If you're in Category 3 (mixed environment), DO NOT attempt to patch your installation. Follow the clean installation process—it's faster and more reliable.You are in Category 1 if ALL of the following are true:
•
NEURON is already installed and launches successfully•
Python (Anaconda or system Python) is installed•
NEURON recognizes Python (you can run simulations via Python)•
You actively run NEURON simulationsIf any of these are false, go to Category 2 or Category 3.
Installation Steps
Step 1: Download BrainCell
All Platforms
1. Visit: https://neuroalgebra.net
2. Download: cloudpackage-v1.zip
o Forum thread: viewtopic.php?t=3
o Note: The ZIP file is password-protected. The password is available on the forum thread above.
3. Create a directory for BrainCell:
C:\braincell
• Right-click cloudpackage-v1.zip → Properties → Check "Unblock" → Apply
Step 2: Compile NEURON Mechanisms (If Needed)
Only perform this step if:• You added new .mod files, OR
• You modified existing mechanism files
Double-click:
build_mechs.bat
If compilation fails: Install Microsoft C++ Build Tools (x64) from: https://visualstudio.microsoft.com/downloads/ (scroll to "Build Tools for Visual Studio")
Then run build_mechs.bat again.
Step 3: Platform-Specific Setup
Windows: Unblock Scripts
Right-click each of the following files → Properties → Check "Unblock" → Apply:
• init.bat
• build_mechs.bat (if you used it)
If Windows blocks execution:
Open PowerShell and run:
Set-ExecutionPolicy -Scope CurrentUser -ExecutionPolicy RemoteSigned
Step 4: Launch BrainCell
Windows
Double-click:
init.bat
Or, using NEURON directly:
nrngui init.hoc
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VerificationAfter launch, you should see:
1. A console window with NEURON initialization messages
2. The BrainCell main window
3. Options to select Astrocyte or Neuron mode
If you see this, installation is complete!
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Category 2 — Clean System Installation
(No NEURON or Python installed)
Who belongs here?
You are in Category 2 if:
•
NEURON is not installed•
Python/Anaconda is not installed•
Fresh OS or minimal systemTypical users: New users, fresh installations, dedicated simulation machines
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Recommended Stable Configuration
For reliable operation across all platforms:
• Anaconda: 2023.09
• NEURON: 8.2.2
• Discussion and updates: viewtopic.php?p=171#p171
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Installation Steps
Step 1: Install Anaconda
Windows
1. Download Anaconda 2023.09:
o Direct link:
o https://neuroalgebra.net/assets/Anacond ... x86_64.exe
o
2. Run the installer:
o Select "Just Me" (not "All Users")
o Use default installation path
o
Check "Add Anaconda to PATH" (important!)o Accept other default options
3. Restart Windows
Step 2: Install NEURON
Windows
1. Download NEURON 8.2.2:
o Direct link:
o https://neuroalgebra.net/assets/nrn-8.2.2-0-setup.exe
o
2. Run the installer:
o Use default installation options
o Install to a simple path (e.g., C:\nrn)
o The installer includes Python interfaces for Anaconda
3. Restart Windows
4. Verify installation by opening Command Prompt:
nrniv -python
You should see the NEURON prompt. Type quit() to exit.
Step 3: Download and Setup BrainCell
Follow the same steps as Category 1, Steps 1-3 for your platform.
Step 4: Compile Mechanisms
Run the build script for your platform (see Category 1, Step 2).
For clean installations, this step is usually required to compile the included mechanism files.
Step 5: Launch BrainCell
Follow Category 1, Step 4 for your platform.
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VerificationYou should see:
1. Console window with initialization messages
2. BrainCell main window
3. Astrocyte/Neuron mode selection
Installation complete!
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Category 3 — Mixed or Incomplete Environment
CRITICAL: Most Common Failure ScenarioWho belongs here?
You are in Category 3 if ANY of the following apply:
•
Python/Anaconda is installed, but NEURON is not•
NEURON is installed, but Python is not•
NEURON cannot find Python•
Multiple Python versions exist on your system•
Previous installation attempts failed•
NEURON launches but BrainCell doesn't workThis is the most common cause of installation problems.
CRITICAL RECOMMENDATION DO NOT:• Attempt to patch your current installation
• Manually edit PATH variables
• Install additional Python versions
• Try to "fix" NEURON/Python integration manually
DO THIS INSTEAD:Follow the clean installation process below.
Clean installation is faster and more reliable than troubleshooting mixed environments.
Clean Installation Process
Step 1: Remove ALL Existing Installations (CRITICAL)This step is mandatory. Skipping it will cause problems.
Windows
1. Uninstall NEURON:
o Settings → Apps → Find "NEURON" → Uninstall
2. Uninstall Anaconda/Python:
o Settings → Apps → Find "Anaconda" or "Python" → Uninstall all versions
3. Remove remaining directories:
o Delete: C:\nrn (if exists)
o Delete: C:\Users\[YourName]\anaconda3 (if exists)
o Delete: C:\Users\[YourName]\AppData\Local\Programs\Python (if exists)
4. Clean PATH variable:
o Press Win, type "environment variables"
o Select "Edit the system environment variables"
o Click "Environment Variables"
o In both "User variables" and "System variables", edit PATH
o Remove any entries containing "python", "anaconda", or "nrn"
5. Restart Windows (critical!)
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Step 2: Verify Clean System
Open a new terminal/command prompt and verify these commands fail:
python --version # Should fail or show system Python only
conda --version # Should fail
nrniv # Should fail
If any of these work, you haven't fully removed the installations. Return to Step 1.
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Step 3: Fresh Installation
Now follow Category 2 (Clean System Installation) exactly as written for your platform.
Install in this exact order:
1. Anaconda first
2. NEURON second
3. BrainCell third
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Advanced Option: Dedicated User Account (Optional)
For the cleanest possible environment, create a new OS user account:
Windows
1. Press Win+R, type netplwiz, press Enter
2. Click "Add" → Create a local account (not Microsoft account)
3. Log in as this new user
4. Follow Category 2 installation steps
macOS
1. System Preferences → Users & Groups
2. Click the lock, authenticate
3. Click "+" to add a new user (Standard account)
4. Log in as this new user
5. Follow Category 2 installation steps
Troubleshooting
Common Issues & Solutions
Issue: BrainCell doesn't start
Symptoms: Double-clicking init.bat does nothing, or window closes immediately
Solutions:
1. Ensure ZIP and batch files are unblocked (see Category 1, Step 3)
2. Run PowerShell command:
3. Set-ExecutionPolicy -Scope CurrentUser -ExecutionPolicy RemoteSigned
4. Try running from Command Prompt:
5. cd C:\braincellinit.bat
Check for error messages
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Issue: Mechanisms fail to compile
Solution: Install Microsoft C++ Build Tools
1. Download from: https://visualstudio.microsoft.com/downloads/
2. Scroll to "Build Tools for Visual Studio"
3. Install "Desktop development with C++" workload
4. Re-run build_mechs.bat
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Issue: NEURON can't find Python
Symptom: NEURON launches but Python commands fail
Platform: All
Solutions:
1. Verify both NEURON and Anaconda are 64-bit
2. Check installation order (Anaconda first, then NEURON)
3. Verify Python from terminal:
4. python --version
5. Test NEURON with Python:
6. nrniv -python>>> import sys>>> print(sys.version)>>> quit()
If still failing: Go to Category 3 and perform clean installation
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Issue: "Module not found" errors
Symptom: Python import errors when running BrainCell
Solutions:
1. Ensure you're using Anaconda's Python:
2. where python # Windows
Should point to Anaconda directory
3. Install missing packages:
4. conda install numpy matplotlib scipy
5. Verify NEURON Python module:
6. python -c "import neuron; print(neuron.__version__)"
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Getting Help
If you're still experiencing issues:
1. Check the full error message in the console
2. Take a screenshot of the error
3. Visit the forum: https://forum.neuroalgebra.net
4. Post your issue including:
o Your operating system and version
o Your category (1, 2, or 3)
o Complete error message
o Steps you've already tried
Forum support typically responds within 24-48 hours.
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Appendix: Command Reference
Quick Commands by Platform
Windows
# Check Python
python --version
# Check Anaconda
conda --version
# Check NEURON
nrniv -python
# Launch BrainCell
cd C:\braincell
init.bat
Summary Flowchart
START
│
├─ Do you have NEURON + Python working? ──YES──> Category 1
│ (Quick setup)
NO
│
├─ Is your system clean (nothing installed)? ──YES──> Category 2
│ (Fresh install)
NO
│
└─ Mixed/partial installation? ──YES──> Category 3
(Clean & reinstall)
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Document Information
Version: 2.0 Last Updated: January 2026 Platforms: Windows 10/11,