Usage Guide

This guide covers everything from your first launch to advanced laboratory workflows.

πŸš€ Quick Start (First Analysis)

Follow these 6 steps to get your first spore count:

  1. Launch MIRA: Open your terminal and type mira.

  2. Connection: Select your camera from the dropdown menu and click Connect.

  3. Working Directory: Choose a folder where your images and Excel reports will be saved.

  4. Load Models: Click Load Models and select the folder containing your YOLO .pt files.

  5. Configure: Toggle the Detection switch. Adjust the Confidence threshold (default 50%).

  6. Capture: Select a chamber on the grid, enter the sample name, and click Capture.

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Main Workflow Details

Once connected, you can fine-tune the image for better detection:

  • Adjustments: Use sliders for Brightness, Contrast, and Saturation.

  • Digital Zoom: Zoom into the center of the frame (1x to 10x).

  • Crop: Fine-tune the visible area with width and height crop sliders.

  • Persistence: Save your settings as a named profile or click Set Default.

The detection engine has three key parameters:

  • Confidence: Minimum probability for an object to be counted.

  • IoU (Intersection over Union): Handles overlapping detections.

  • Dense Mode: Toggle this for high-density samples. When enabled, MIRA:

    • Switches to a tighter IoU threshold (0.5) to separate closely packed objects.

    • Enables agnostic NMS (Non-Maximum Suppression across all classes).

    • Uses a denser tracker configuration (BotSORT on GPU, ByteTrack on CPU).

    In sparse mode (default), the tracker is optimized for speed with lower overhead.

MIRA supports multiple counting standards. Select the method in the Chamber Selection panel:

  • Malassez: 40 rectangles (Γ—2,500), 20 rectangles (Γ—5,000), or Full Grid β€” 100 rectangles (Γ—1,000).

  • KOVA: Big Square (Γ—5,000) or Small Square (Γ—90,000).

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Advanced Features

🧬 Serial Dilution Workflow

If your sample is too concentrated, use the Dilution tool:

  1. Click the Dilution button β€” it enters dilution mode (stays toggled).

  2. Click the target chamber on the grid.

  3. Enter the dilution factor (e.g., 100 for a 1/100 dilution).

Result: MIRA multiplies the detected count by this factor in the final Spores/mL calculation. The factor is stored per chamber and included in the Excel export.

⏱️ Batch Capture

To increase statistical reliability, capture multiple images of the same chamber automatically:

  1. Open the Chamber Images window (double-click a chamber on the grid).

  2. Click Batch Capture.

  3. Set the number of images (1–50) and delay between captures (1–10 seconds).

MIRA captures each frame automatically with a progress bar, then saves and analyzes all images in the sequence.

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Keyboard Shortcuts

Boost your productivity with these built-in shortcuts:

Shortcut

Action

S

Toggle Camera Start/Stop

D

Toggle Object Detection ON/OFF

C

Capture current frame (or add image when chamber window is open)

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πŸ’‘ Important Note on Lighting

For optimal YOLO detection, ensure your microscope lighting is Koehler-aligned and the background is as uniform as possible. Shadows or uneven light can affect confidence scores.