MRI_Analyze_Comets_Tool

The tool estimates the number of comets per cell.

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.

• 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.

Options

Cell Segmentation

comets channel

The number of the channel containing the comets.

other channel

The number of another channel in which the cells are stained. If none use the same number as for the comets channel.

sigma Gaussian blur for cell detection

The sigma of the Gaussian blur filter used for the cell segmentation. If cell are not separated, try a smaller value.

thresholding method for cells

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

proeminence for maxima detection

The proeminence of the maxima for the seeded watershed.

Border Correction

delta x for border direction

The distance betwwen points used to calculate the perpendicular direction for the border points.

radius for border correction

The radius around the border points in which the minima a searched to correct the border.

line width for profile

The width over which the profile plot is averaged when searching for the minima to correct the border.

min. tolerance minima detection

The tolerance used when detecting the minima in the profile

Comets Segmentation

min. size comets

The minimum area for a particle to be considered a comet.

thresholding method for comets

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