CaviTools: Automated processing of xylem cavitation and optical dendrometry image sequences | Version 1.1

The tools build on Chris Lucani's work at https://www.opensourceov.org/ and use the image stabilisation software vidstab by Adam Spannbauer.

To process and analyze image stacks based on the optical method can be challenging, especially with large datasets. Additionally, we have found that not all brightness differences between images correspond to cavitation events. Camera shifts, resin flow, and insects passing through the frame can lead to wrong events. Manually reviewing all images to filter out these artefacts can be very time-consuming. Therefore, we offer the following tools to simplify the workflow of post-processing your data:

• Automated analysis determining the percentage of cavitated xylem area in stem- or leaf image time series
  • Possibility to individually calibrate processing parameters handling noise
  • Classifier that detects <ins>vertical</ins> stem embolism events and automatically cleans results from artefacts
• Automated analysis of area change in optical dendrometry image time series
• Output: Processed images and result datasheets (.xlsx, .csv)
• Resource efficiency: around 250 images per minute are processed utilizing approximately 300MB of RAM

More info: https://zenodo.org/records/13328771