RRQuant

Image processing workflow for the analysis of ruthenium red stained Arabidopsis dark grown hypocotyls.

Installation

• Requirements:
  • Fiji (https://imagej.net/software/fiji/downloads)
  • MorpholibJ Plugin (https://imagej.net/plugins/morpholibj)
• Fiji macros:
  • Copy the RRQuant_Workflow_toolset.ijm file to your Fiji "macros/Toolset folder".
  • Access the tools from the right end side of Fiji window ">>" (More tools).
• R Script:
  • See the userguide (https://github.com/VergerLab/RRQuant/blob/main/UserGuide_RRQuant_Rscript.pdf)

Usage

Starting from large tile stereo microscope images of ruthenium red stained samples.

1. Split large images per genotype/condition, stained/non-stained, replicates (SplitLargeImage.ijm).
2. Run segmentation with root painter (https://github.com/Abe404/root_painter/tree/master), using our model trained for RR stained hypocotyls segmentation (RRQuant_DarkHypo_RPWeight_V1.pkl).
3. Convert/correct root painter masks (MaskConvert.ijm).
4. Run staining intensity and morphometrics quantification (RRQuant.ijm).
5. Analyze data with R (RRQuant_data-table.R and RRQuant_app.R).

All ImageJ Macro (SplitLargeImage.ijm, MaskConvert.ijm and RRQuant.ijm) are packaged in an imageJ toolset laid out from left to right, but the individual macro soucres are also available in the macros folder.