Lab Slice Manager

A web-based application for managing mouse brain slices and experiments in the lab.

Current Version: 3.0

Features

• 🐭 Mouse Database - Track mice with ID, sex, genotype, birth date, sacrifice date
• 🧠 Slice Tracking - Record brain slices with region, thickness, cryosection date, embedding matrix
• 🧪 Multi-Slice Experiments - Link multiple slices to a single experiment with per-slice treatments
• 🏷️ Label Printing - Generate and print labels with experiment ID, mouse info, and treatment
• ☁️ Cloud Sync - Automatic synchronization via Supabase (optional)
• 📱 Works Everywhere - Use on any device with a web browser
• 💾 Backup/Restore - Export and import data as JSON files
• 🔒 Magic Link Auth - No passwords to remember

What's New in v3.0

Major Architecture Change: Experiments now support multiple slices from different mice!

• Create experiments first, then add slices to them
• Or start from a slice and create/join an experiment
• Each slice in an experiment has its own treatment/protocol field
• Compare slices from different mice in the same experiment
• Print labels showing experiment + slice + treatment info

Quick Start

Offline Mode (No Setup Required)

1. Download index.html
2. Open in any web browser
3. Click "Continue Offline"
4. Start using!

Online Mode (Cloud Sync)

See the Deployment Manual for complete setup instructions.

Files in This Repository

File	Description
index.html	The main application
DEPLOYMENT_MANUAL.md	Complete setup and usage guide
ARCHITECTURE.md	Technical documentation
CHANGELOG.md	Version history and changes
fresh_schema_v3.sql	Database schema for new installations

⚠️ Upgrading from v2.x

Version 3.0 requires a fresh database schema. The old experiment structure (one experiment per slice) is incompatible with the new many-to-many architecture.

Before upgrading:

1. Export your data from v2.x (Database icon → Export)
2. Save the backup file safely
3. Note: Old experiments will need to be re-created manually

To upgrade:

1. Run fresh_schema_v3.sql in Supabase SQL Editor (this drops old tables!)
2. Replace index.html with the new version
3. Re-enter data or selectively import mice/slices from backup

Data Model

┌──────────┐      ┌──────────┐      ┌───────────────────┐      ┌─────────────┐
│  MICE    │──┐   │  SLICES  │──┐   │ EXPERIMENT_SLICES │   ┌──│ EXPERIMENTS │
│          │  └──▶│          │  └──▶│   (junction)      │◀──┘  │             │
│ M-XXXX   │      │ S-XXXX   │      │ treatment field   │      │ E-XXXX      │
└──────────┘      └──────────┘      └───────────────────┘      └─────────────┘
   One              Many               Many-to-Many              Independent

Tech Stack

• Frontend: React 18 (via CDN)
• Styling: Tailwind CSS
• Backend: Supabase (PostgreSQL + Auth)
• Hosting: GitHub Pages (or any static host)

License

For lab use. Feel free to modify for your needs.