Measure the relative area of sirius red stained fibrosis. The tool uses the colour deconvolution plugin from Gabriel Landini.

You can find test images here and here.

To install the tool, drag the link MRI_Fibrosis_Tool.ijm to the ImageJ launcher window, save it under macros/toolsets in the ImageJ installation.

Select the "MRI_Fibrosis_Tool" toolset from the >> button of the ImageJ launcher.

• the first button (the one with the image) opens this help page.
• the m-button runs the analysis on the active window. Note that you should crop the image and that there should be a selection (roi) on the cropped image.
• the b-button runs the analysis on a folder containing cropped images with a selection (roi) in tif-format.

Right-click on the m-button to open the general options dialog:

• r1, g1, b1 - the RGB-components (between 0 and 1) of the colour we want to segment.
• r2, g2, b2 - the RGB-components (between 0 and 1) of the first background colour.
• r3, g3, b3 - the RGB-components (between 0 and 1) of the second background colour.
• file ext. - the file extension (including the dot) of the input files

Right-click on the b-button to open the batch-options dialog:

• control folder - the name of the sub-folder into which the control images will be saved
• results table - the name of the results table and the results spreadsheet file (csv text saved as .xls)

Colour deconvolution is used to separate the staining into a single image. A simple auto-threshold with the default method is applied and a selection is created. The area of the selection is measured and compared to the area of the selection on the input image. The colour deconvolution is done using the Colour Deconvolution Plugin¹ from Gabriel Landini

Note that you can use the colour deconvolution plugin if you need to find different colour vectors. You can then enter the new values in the options dialog or change the default values in the macro's source code.

1: ImageJ.net - Colour Deconvolution

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1. Mondor Biomedical Research Institute

2. Fibrosis (bio-protocol exchange)

1. Medindo fibrose com ImageJ/Measuring fibrosis with ImageJ (Portuguese)