LHP1 data analysis

Repository holding analysis scripts and pipelines for analysing LHP1 roots using a novel pipeline

The repository also contains diagnostic and visualisation tools for testing the pipeline.

Method

This pipeline requires both root images and segmentations (which can be produced by dtoolbioimage).

The pipeline carries out the following steps:

1. Load the cell wall and venus channels from the image datasets as 3D images.
2. Scale these images to correct for differences in physical size to voxel size conversion along axes.
3. Load segmentation for the image.
4. Removes all segmented regions touching the border of the image.
5. Order segmented regions by volume and take the top n (300 by default) regions.
6. Measure and report the mean FLC-Venus intensity in each segmented cell.