At this point you should have a sequence of high resolution images of the xylem. If you don’t, head over to capture for information and resources. More information about the technique and OpenSourceOV project in general can be found in the overview.

Processing the captured sequences involves extracting the differences between pairs of images in the sequence, removing noise and any artefacts (such as a insect walking across the sample!), and quantifying the degree of embolism in each image.

Instructions for processing can be found below. Note that this will take you to Github where all the written resources are hosted and managed. Github is a tool for collaboration, and OpenSourceOV is an Open Source project which means anyone can contribute to improve any of the resources – even if that means correcting a spelling mistake. Check out the contributing page for more information.



Processing Instructions


ImageJ Toolbox




Help improve these resources by contributing to the project.


Sample selection and preparation

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Eucalyptus regnans stem
Captured by Chris @ the Brodribb Lab. This is the sequence before processing. Large sequence (~9MB) - may need to wait for it to load to run smoothly.