Tutorial

Scripting using ImageJ (Fidji)

Fidji is an image processing package, that can be described as a distribution of ImageJ, but with more features.It allows to write scripts and record the commands.

1. Start-up the script editor [PlugIns -> Scripting -> Script Editor]

and set the language [Language -> ImageJ macro]

2. Syntax of the macro:

macro "name of macro" {

print("Hello World!");
}

3. Install the macro in ImageJ or Fiji. In the Editor menu [Run -> Install Macro]

4. In Fiji menu:  [Plugins -> Macro -> name of macro]

5. Save the macro. [File -> Save As...]

6. To include ImageJ Macro Commands into your macro you can use “Macro Recorder”

This is a tool for macro programming, the changes you apply to your image are wrote down into commands in the Recorder window. You can then transform them into a macro.

[PlugIns -> Macros -> Record...]

 

For a more detailed tutorial: http://cmci.embl.de/_media/documents/slides/elmi2012.pdf

 

 

Script for Prototype I

First of all, make sure that the name of the blank measurement is: Blank.JPG

Then you might want to change the paths directory in the script (for blank, sample image and results) and the number of images you want to analyze (frames = 7). For each image, you will need to enter its name.

To install and then use the script: [Plugins -> Macro -> Install], then [Plugins -> Macro -> Biodesign]