MRI_Analyze_Comets_Tool

The tool measures the areal number density of comets in cells.

You can find the tool's source code here.

Getting started

To install the tool save the file analyze_comets_tool.ijm under macros/toolsets in your FIJI installation.

Select the analyze_comets_tool toolset from the >> button of the ImageJ launcher. You need to have FeatureJ installed.

• The first button on the toolset opens this help page.
• The a-button runs the analysis on the current image.
• The b-button runs the analysis on all the images in a given folder.

Method

The comets are segmented and the binary mask is skeletonized. The end-points of the skeleton are marked and the number of end-points divided by two is given as an estimation of the number of comets.

Options (analyze image)

Right-click on the a-button to open the options-dialog.

Stack layout

red channel

The number of the channel in which the cells are stained.

comet channel

The number of channel containing the comets.

nuclei channel

The number of channel containing the nuclei.

z-slice

The number of the z-slice that will be used for the analysis.

Cell segmentation

min size

Smaller objects will not be considered cells and will be removed from the analysis.

min. intensity red

Cells with a smaller mean intensity (in the nucleus area) will be removed.

thresholding method cytoplasm

The auto-thresholding method used for the segmentation of the cells (the cytoplasm).

Comet segmentation

min. size comets

Smaller objects will not be considered comets and will be removed from the analysis.

max. circularity comets

Objects more circular will not be considered comets and will be removed from the analysis.

thresholding method comets

The auto-thresholding method used for the segmentation of the comets.

number of dilates

After segmentation and before skeletonization a number of dilate operations is executed, followed by a number of erode operations.

number of erodes

After segmentation and before skeletonization a number of dilate operations is executed, followed by a number of erode operations.

Options (batch analysis)

file ext.

The file-extension of the input images.