Germination Analysis – Arabidopsis thaliana (Screening Interface)
Interface Components
- Project Directory: Specifies the storage location for your analysis results. A project encompasses a complete experimental setup involving one or more Raspberry Pi modules.
- Video Directory: Identifies the video file for current processing. Videos must be processed sequentially, one at a time.
- Analysis Identifier: Identifies the current plate being analyzed.
- Time Between Slices: Sets the temporal resolution of the Raspberry Pi module.
- Extra Time Before First Picture: Accounts for additional time lost when plates are removed from cold storage or placed under light conditions, ensuring accurate germination timing calculations.
- End germination plot time (hours): Specifies the cutoff time for germination analysis.
- Calibration Settings: Converts measurements from pixels to millimeters for accurate dimensional analysis.
- Processing options: Allows selection between different analysis modes, such as germination, plant measurements and fpca analysis. Includes a button to store tracking visualizations for quality control.
- Group Names: Assigns variety identifiers to groups of seeds for experimental organization.
1. Getting Started
Begin by creating a dedicated folder for storing results, then select the first video from the Demo dataset. A popup window will prompt you to choose the appropriate folders.
2. Video Preview and Configuration
Click the "Preview Video" button to view your selected video. Navigate between frames using the scrollbar and press the "S" button to toggle the segmentation overlay for visual inspection.
3. Calibration Setup
As this video does not have proper QR codes that are visible, we will need to manually calibrate the pixel-to-millimeter ratio.
Measure a known distance for calibration purposes. In this example, the left-to-right distance spans 11 centimeters. Use the calibration tool to determine the pixel-to-millimeter conversion ratio, particularly when QR codes are not present on the plate.
4. Processing Options
Select the "Germination" processing option to focus the analysis on germination events. Turn off other processing options that are not relevant for this experiment.
5. Group Configuration
Configure the four seed groups according to your experimental design. Complete all group assignments as shown in the interface.
6. ROI Selection
Use the ROI (Region of Interest) tool to define analysis areas for each seed group individually.
7. Results Monitoring
Navigate to the Results tab to monitor processing status and track analysis progress.
8. Generating Report
Click "Generate Report" to generate the comprehensive final report containing all germination analysis data.
If the video was too long, and the germination time is too cramped at the beginning of the plot, you can adjust the "End germination plot time (hours)" parameter and reprocess the video to obtain a clearer visualization of germination events. Then, click "Generate Report" to update the report.
