Intranet PHIV

PHIV_Rootcell_toolset

Toolset for semi-automatic measurement of several parameters on images of (rice) root transverse sections
(Front Plant Sci. 2014; 5: 790. Published online 2015 Jan 19. doi)

PHIV_Rootcell_toolset.txt (save in ImageJ/macros/toolsets)
User Manual

Install plugin: Polar_Transformer.class

Parameters

This first optional tool will ask you to choose if you want the verbose mode or not (default = Yes), and which type of images you are analysing. Microscopy Fluorescence or Bright-field (default: Fluorescence). We have developed the PHIV-RootCell toolset specifically for fluorescence images. However, depending on your image, you can change the default parameter ("Fluorescence") or "Bright-field".

Root Selection

This first tool will automatically select the entire root area.

Stele Selection

This tool will draw an oval selection in the middle of the Root Selection. The size of the oval selection is a parameter of this tool defined as the proportion RootArea/SteleArea (right click, default = 4)

Xylem Selection and Count

This tool will automatically select the central metaxylem area and count the number of central metaxylem vessels.
in option (right clic):
- Gaussian Blur (default = 2)
- Selection smooth (default = 2)
Metaxylem : to count the number of metaxylem vessels

Cortex Selection

his tool will automatically select tissue area internal to sclerenchyma (brighter fluorescence)
in option (right clic):
- Gaussian Blur (default = 2)
- Selection smooth (default = 30)
- EDM factor : Multiplicate Euclidean Distance Map before substracting from Image (default = 1)

Layer and Cell File Counts

This tool will first do a polar transformation of the original image.
The number of cell layers and the number of cells in a particular cell file will be respectively defined by the number of maxima detected on vertical and horizontal lines in the polar transformed image.
This modification of the image will allow to count the number of cell layers (average of n measures, n defined by user in option) and the number of cells in 1 or several cell files (number of cell files to be analysed defined by user in option)
in option (right clic):
- Noise tolerance of find maxima (default = 20)
- Number of measures to be recorded to count the number of cell layers (default = 3, average of these n measures will be reported in the Analyses table)
- Number of measures to be recorded to count the number of cells in cell files (default = 3, each of these counts will be recorded in the Analyses table)

Display data

This tool will display and save the image with selections and the Roi Manager in the original image directory. All the measurements are also display in the "Analyses" window (Table headings: Picture / RootArea / ExternalLayerArea / CortexArea / SteleArea / CentralMetaxylemArea / NbCentralMetaxylem / NbMetaxylem / MeanNbCortexLayers; with "NA" values if none).

New image

This tool will close all images and reset the ROI Manager. The file manager will go to the directory previously opened to select a new picture for analysis.