This library is meant to be distributed as an extra module of the Fiji software. Right now, it ships:
A Fiji plugin that can open conjointly an image sequence, and a spectrum file (in the shape of a CSV file) and display both image and spectrum simultaneously.
A TrackMate action that performs the analysis of the velocity of moving particles. It allows for the detection of pauses and runs in tracks, and assign a movement type to track segments. Extra velocity features are added to benefit from this analysis.
A TrackMate view that specializes on image sequences made of single line frames. It displays the profile of a frame and the kymograph of the image sequence.
Binaries are distributed through the ImageJ updater.
Go to the menu item Help > Update. Update and relaunch Fiji until you are completely up to date.
When done, go one more time to the updater (Help > Update) but this time click on Manage update sites.
On the new window that appear, click on Add. A new line appears
at the bottom of the sites listed. Update the two first
columns with Optofluidics for name and
http://sites.imagej.net/Optofluidics.
Then click elsewhere to validate the content.
Fiji should block a little while it is querying the update site.
Click on Close. In the main updater window, the View option
list should show a new site, with a single jar file in it:
Optofluidics.jar.
Click on Apply changes. Restart Fiji. In the Plugins menu you should notice a new Optofluidics menu. Right now, there is only the Spectrum player. ckMate modules will appear when running the TrackMate plugin.