Neuroalgebra forum

BrainCell Installation Guide

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 simulations
If 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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Verification
After 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 system
Typical 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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Verification
You 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 Scenario
Who 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 work
This 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,