README.md

ImmunofluorescenceAnalysis

Fiji macro for immunofluorescence analysis

Run the macro here in Fiji software

https://imagej.net/software/fiji/downloads

AnalyzeParticleAbeta.ijm

There are two ways of analyzing image(s).

1.Open your image and run the macro.
Images should be cropped before analysis.

2.Run the macro then choose a directory that has images you want to analyze.

An example image of Amyloid-beta staining.

Here the process;

1. Enter the region name you want to analyze in a dialog box.
   

2. Set ROI you want to analyze, then click [OK] button.

3. Ready to automatically save the result of analyze particle function.
   The result will be stored in the same hierarchical directory as the analyzed image.

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ProcessFolderNeunPsdAnalysis.ijm

First, run the macro then choose a directory that has images you want to analyze.
This macro can set a ROI.

This version accepts RGB stack image only.
The stack level should be like the following;

• NeuN channel1 (green)
• PSD95 channel3 (red)
• channel2 (blue) is not used

If your images are not in this order, change the channel numbers in line 114-116 of the macro to match your images.

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ProcessFolderAbetaMicrogliaOverlapAnalysis.ijm

First, run the macro then choose a directory that has images you want to analyze.
High magnification or cropped images are preferable.

Here is an example image.

Green = Iba1
Magenta = Amyloid-beta (Methoxy-X04)

Measurement results of area%, size and so on, of amyloid-beta, microglia will be automatically saved at the present path (the same hierarchical directory as the image).
Calculates ratio of double-positive area of amyloid-beata and microglia to microglia.