Example macros (.ijm) and jython scripts (.py) demonstrating useful functions provided by the ACQUIFER update site in Fiji (freely available upon request), or more generally by the ACQUIFER java packages.
Some of these examples are also shipped by the update site, and are available in the menu Acquifer > Examples.
The examples can be opened and run in Fiji, by drag and dropping the script file on the Fiji window.
Currently for the ImageJ macro-language, the examples cover the extraction of metadata from the image file name (see examples > MetadataParsing).
The jython scripts demonstrate a larger panel of functions available in the Java API, which can be reproduced in other scripting languages supported by Fiji.
For the scripting examples, some functions are specifically available for Fiji (ex: hyperstack), while others such as metadata parsing are not depending on Fiji and thus could be used in other java software such as QuPath or ICY.
You can download this repository by clicking the green button "code" and select "Download zip".
Alternatively if you use GitHub, you can fork this repository to customize these examples to your need.
You can also download single files by clicking the filename, then the "raw" button at the top left of the page, and finally right-click, save as.
You can find more documentation about the different ressources used in these examples on the following pages:
- Metadata encoding in image filenames
- Batch-processing plugins
- Processing individual image-files in batch
- Hyperstack plugins
- Acquifer Java packages
- acquifer-core java API documentation (compatible with any Java program)
- acquifer-IJ java API documentation (custom scripting ressources for ImageJ/Fiji)