This Maven project implements ImageJ 1.x plugins for time sequences:
- Temporal median: finds moving foreground features, see Parton et al. (2011), JCB 194 (1): 121.
- Trails: does simple averaging over a time window, making tracks visible.
The plugins ought to work for hyperstacks.
Free software, released under the GNU General Public License, http://www.gnu.org/licenses/gpl.html
Copyright Graeme Ball (2013), [email protected], written while working at Micron Oxford: www.micron.ox.ac.uk
Latest .jar files for DOWNLOAD on the Micron Oxford Website
The maven project structure is derived from: https://github.com/imagej/minimal-ij1-plugin
This plugin can be used to find moving foreground features, which can be be a powerful way to suppress false background detections in subsequent tracking steps.
- set time window, and standard deviations above background for foreground
- time window should be more than 2x larger than time taken for a feature to traverse a pixel (NB. total window is 2x half-width +1)
- moving foreground identified by intensity increase relative to background average (i.e. median) for a pixel over a given time window
- "soft" segmenation, yielding foreground probability related to excess intensity (in standard deviations) over background level
- crude Anscombe transform applied to data to stabilize the variance
Averaging a short time window can be useful for enhancing signal-to-noise, and longer time windows can be used to create trajectory snapshots.
- set a time window over which to average slices