Add Guava Muse SOP protocol documentation and update navigation

Author: kubu4

docs/protocols/protocol-guava_muse.md

@@ -0,0 +1,101 @@
+# Guava Muse SOP
+
+The Guava Muse Cell Analyzer provides automated cell count and viability measurements. These protocols cover setup, daily operation, and maintenance.
+
+It is highly recommend you read through the manufacturer's protocol prior to using the machine!
+
+- [Cytek-muse-guava-cell-analyzer.pdf](https://github.com/RobertsLab/resources/blob/master/equipment_manuals/Cytek-muse-guava-cell-analyzer.pdf) (GitHub)
+
+## Kits Used
+
+- **Muse System Check Kit**: Verifies the performance of the system by assessing counting accuracy and fluorescence detection using a standardized fluorescent bead reagent. The kit contains a bead reagent and diluent.
+- **Muse Count & Viability Kit**: Used to determine viability and total cell count. Accurate assessments can be made with a wide variety of cell lines, even those with unusual culture conditions or a tendency to aggregate.
+
+---
+
+If this is the first time the machine is being _ever_ being used, please see [Instrument Setup Section](#instrument-setup-first-time-only).
+
+## Daily Startup Procedure
+
+1. **Turn On Unit**
+   - Press power button if not auto-on. Wait for touchscreen to initialize.
+
+2. **Prepare Fluids**
+   - Empty waste bottle, rinse, and refill with 10 mL bleach.
+   - Refill cleaning bottle with Guava ICF to indicator line.
+   - Reconnect fluid tubing.
+
+3. **Reset Fluid Levels**
+   - On touchscreen: `Menu` → `System Check` → `Clean` → `Reset Fluid Levels`.
+
+4. **Run Complete System Clean**
+   - On touchscreen: `Menu` → `Muse System Cleaning` → `Complete System Clean`.
+   - Load full tube of Guava Instrument Cleaning Fluid (ICF) → then DI water.
+   - Run until log confirms success.
+
+5. **Run System Check**
+   - Mix beads prior to making solution.
+   - Prepare 1:20 dilution of System Check Beads.
+   - On touchscreen: `Menu` → `Essential Tools` → `System Check`.
+   - Enter Lot #, Expiration, Check Code (found on bead kit card).
+   - Mix beads, load tube, run 3 replicates.
+   - Confirm **PASS** status and %CV ≤10%.
+   - Export results (optional).
+
+> **Note**: The values recorded during the replicates should be green/grey, meaning they fall within the expected range. If they are red, the values are too high/low, and the system check will fail. This check is temperamental. Values should be within $4.5 \times 10^4$ - $5.5 \times 10^4$.
+
+---
+
+## Daily Shutdown Procedure
+
+1. **Run Complete System Clean**
+   - Same as startup. Ends with DI water rinse.
+
+2. **Leave DI Water Tube on Loader**
+   - Never leave bleach or ICF on the system overnight.
+
+3. **Power Down**
+   - On touchscreen: `Menu` → `Power Options` → `Power Off`.
+
+---
+
+## Maintenance Log Example
+
+| Date | User | Waste emptied | ICF refilled | System Clean | System check (p/f) | Notes |
+| :--- | :--- | :--- | :--- | :--- | :--- | :--- |
+| 18/04/25 | Aakriti | No | Yes | Yes | Pass | First use so did not empty waste |
+| 21/04/25 | Aakriti | Yes | Yes | Yes | Pass | |
+| 24/04/25 | Aakriti | Yes | Yes | Yes | Pass | |
+
+---
+
+## Important Usage Notes
+
+- **Quick Clean**: When running samples, need to run a quick clean every 20 acquisitions.
+
+--
+
+## Instrument Setup (First-Time Only)
+
+1. **Unpack and Position**
+   - Carefully remove the Muse from the shipping box and save all packaging.
+   - Place it on a stable surface away from vibrations.
+
+2. **Connect Fluid Bottles**
+   - Connect color-coded fluid tubing to the back of the instrument.
+   - Fill waste bottle: add ~10 mL bleach (to first fill line).
+   - Fill cleaning solution bottle to the indicator line with Guava ICF.
+   - Insert bottles into their matching receptacles and connect the tubing.
+
+3. **Insert Flow Cell**
+   - Open the access door and follow flow cell insertion.
+
+4. **Power On**
+   - Plug the Muse into a grounded outlet. It turns on automatically the first time.
+
+5. **Log On as Administrator**
+   - Select Administrator account on first login (p. 35).
+   - **Important**: Add a new Admin-level user to avoid losing access to data.
+
+6. **Initial Cleaning**
+   - Run **Complete System Clean** → do this twice on first use (On touchscreen: `Essential Tools` > `Complete System Clean`) (p. 63).

mkdocs.yml

@@ -87,6 +87,7 @@ nav:
      - Lab Protocols:
        - Bullet Blender: 'protocols/protocol-bullet_blender.md'
        - Glycogen-Glo Assay: 'protocols/protocol-glycogen-glo-assay.md'
+       - Guava Muse SOP: 'protocols/protocol-guava_muse.md'
        - qPCR: 'protocols/protocol-qPCR.md'
        - Resazurin Assay: 'protocols/resazurin-assay.md'
        - Reverse Transcription: 'protocols/protocol-reverse_transcription.md'