ExoU
Download
GUI
In the main dialog, the most important parameters to change are: “Downscale image by a factor” and “Difference map threshold”. The rest of the parameters can be kept as given by the plugin.
To get some idea about the appropriate value for the Difference map threshold, check the histogram plot (press the List button to get the actual values in the histogram bins) that will indicate the distributions of the maxima per frame (in many frames those maxima will be just largest noise spikes and only in a few they will correspond to the actual events which are by definition the highest in the amplitude)
NOTE: To let the plugin find that threshold automatically put 0 (zero) in the field “Difference map threshold” of the main dialog of the plugin.
When processing is finished, hover the mouse pointer on one of the patches in the tiled window (see the image below, right) and press “g”, the intensity profile for that specific location will be automatically displayed in the “time traces” plot. Other keys that work are “b” – label the event/square as inactive, “t” – update the table taking into account only the active events (not the ones that were great out with “b” key), “s” – save 3 images and the result table to the folder. Later on it is possible to open those files and continue with the interactive analysis using the plugin “ExoU (Manual Correction)”
How to install
- check if “imagescience” library is already installed in Fiji. Go to “”Help”> “Update” > “Manage Update Sites”, check the “ImageScience” site and press “Apply and Close”
- copy “cilia_.jar” into the “plugins” folder of the Fiji installation on the disk, Restart Fiji.
- to run the analysis go to “Plugins” menu and select “CELMIA” > “Synaptic Spark”
If Fiji crashes because of the memory issues, go to “Edit” > “Options” > “Memory and Threads” and increase the memory size as much as you can (taking into account the size of the physical RAM installed on your PC or laptop.