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Practical: Viewing volumetric data

A short practical on viewing volumetric data in Fiji
A screenshot of orthogonal views in Fiji derived from an image stack of a flourescent marked confocal image stack of an Arabidopsis plant root.

Software such as Fiji offers several ways to view and manipulate 3D volumetric image data.

This practical lets you try out a few, as well as performing some analysis on the data using the 3D object counter.

All the instructions are in the attached pdf Viewing volumetric data.

The image data used in the practical is Arabidopsis_confocal.tif and can be found at https://github.com/nlmellor/PhenoDataCampp/tree/main/ImageAnalysis/data.

Please let us know how you get on in the comments.

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Introduction to Image Analysis for Plant Phenotyping

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