imagej-macro

This is a collection of ImageJ1 macro that we found useful for analysing images acquired on optical microscopes enabling the quantification of biological processes.

Requirement

• We use Fiji (ImageJ 1.53c) to develop the macros https://imagej.net/Fiji.
• Some macros use script parameters https://imagej.net/Script_parameters

Content

Click on the macro name to access the raw macro file that you can save on your computer or click on the description to access the documentation page.

Macro Name	Description
Align_channels.ijm	Align Channels using beads
Detect_3D_Spots.ijm	Detect and count spots in 3D
Colocalization_Analysis.ijm	Colocalization in ROIs
Local_Colocalization_Coefficient.ijm	Local (Pearson & Overlap) colocalization coefficient
GUV_Intensity_Region.ijm	Analysis of intensity over time of GUVs with a region based approach
GUV_Intensity_Contours.ijm	Analysis of intensity over time of GUVs with a contour based approach
FRAP_Measure.ijm	FRAP measurement with manual tracking
Beads_FWHM.ijm	Measure the FWHM of fluorescent beads
Convert_File.ijm	Convert files and apply simple transformation
Export_Series.ijm	Export series from a multi-image container (LIF file)
Cilia_Beat.ijm	Analysis of Cilia Beats
Tile_Tools.ijm	Manipulate tiles

Otherwise,

• browse the folder,
• click the individual file you want to download,
• press the raw button
• download the raw file (Ctrl-S) and open in in ImageJ/Fiji