An ImageJ plugin to generate kymographs with a live preview
A kymograph is an image that represents spatio-temporal data on a single frame instead of on an animation. You will find information about Generating and exploiting kymographs on the ImageJ tutorials.
ImageJ/Fiji has several built-in features to generate kymographs, and many plugins also exist. I created this one to gather features that I find useful when analysing data with kymographs:
- A live preview of the kymograph about to be generated, also featuring an indication of the on-screen frame on the temporal axis.
- A kymograph annotation tool, to mark interesting time periods in kymographs generated from time-lapses featuring many events.
- A direct annotation of the source image, marking the spatio-temporal coordinates of the interesting time periods in kymographs.
The annotation parameters will be saved in a table, such that you can import the ROI later. In addition, kymographs pixels are calibrated from your original data. Pixel width will correspond to spatial scale, while pixel height will correspond to frame interval.
Missing features:
- Removal of ROIs from the table is not supported yet. A possible way to implement this features is described by the author of TrackMate on the image.sc forum.
- Wide ROIs extending outside the image will have incorrect pixel values.
- RGB input time-lapses raise an ImageJ error.
Contributions are welcome!
How to install
You can add this Plugin to your ImageJ/Fiji installation either by configuring an Update Site in ImageJ/Fiji, or by installing it manually.
5 clicks procedure: the easiest way is to use the Update Site.
- As stated in the official ImageJ documentation, you can navigate in ImageJ’s menu to
Help > Update.... - Then click on the
Manage update sitesbutton. - In the list that opens, find the entry named Live-Kymographer and tick the checkbox.
- Fiji will now display the changes it has to perform to install the plugin. If the list is very long, I would recommend reading this page on ImageJ’s wiki. Otherwise, simply click on
Apply changes - Restart ImageJ, and you’re done.
Manual installation: even-though the procedure is described with fewer steps, it requires more autonomy from your side. With this method, you can install any version of the plugin, but it will not be updated automatically by ImageJ.
- Head on to the Releases page here on GitHub.
- Download the
.jarfile for the latest version (or another one). - Copy this file into your ImageJ/Fiji plugins directory. This directory is located in your ImageJ/Fiji installation, but I cannot tell where that is as it depends on the systems.
- Restart ImageJ, and you’re done.
