Note: please read the License Information file for details about licensing and use. By using this software, you are agreeing to the license agreement.

Fiji update site (recommended).

I have an update site for FIJI (https://research.stowers.org/imagejplugins/updates/). See the fiji help guide to follow the site with your copy of FIJI. This is the recommended installation mechanism as it provides update reminders and will install dependencies. Note that due to recent server security updates, the former Fiji update site URL does not work. You need to either manually change it to https://research.stowers.org/imagejplugins/updates/ or reinstall a fresh copy of Fiji which should have the correct URL.

Download Files (advanced users).

All plugins can be downloaded as a jar file here: Jay_Plugins.jar. For installation, simply copy this file to your plugins folder.

I used to have the packages Jay_Plugins2.jar and Jay_Plugins3.jar but modern ImageJ supports a larger number of plugins so those plugins have been shifted into the Jay_Plugins package.

The source code can be accessed by opening the above jar files with any zip archive utility (e.g. 7-zip). The source code can be browsed here. The API can be browsed here. If you prefer github, I have a library there as well.

A zipped documentation folder is here: Docs.zip.

Here is an excel worksheet with a list of plugins and a brief description: Plugins_List.xls.

Note that these plugins are provided on an as is basis with no guarantees or support. A common problem with my plugins is that most are written for 32-bit images with support added later for 16 and then 8 bit images. If you get an error that says "[S cannot be cast to [F" or "[B cannot be cast to [F" then you need to convert to 32-bit with Image>Type>32-bit. Updates for the plugins will be uploaded periodically. The individual user is responsible for updating. I will make an effort to maintain backward compatibility, but there is no guarantee of this, so a backup copy should always be made before updating.