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cmeAnalysis / clathrin-mediated endocytosis analysis
Allows quantification of clathrin-coated pit dynamics from fluorescence time-lapse data. cmeAnalysis provides functionalities including: (1) sensitive detection, (2) tracking (based on u-track), (3) master/slave detection for multi-channel data, (4) intensity-based classification of coated structures, and (5) lifetime analysis. It also contains a graphical user interface (GUI) for inspection of analysis results from individual movies.
TraJClassifier
Supports local analysis and is able to split a single trajectory into segments with different motion types. TraJClassifier is a Fiji plugin providing a practical and device-independent method to classify and segment particle trajectories into four main motion types. It loads trajectories from TrackMate (exported via the action "Export trajectories"), characterizes them using TraJ and classifies them into normal diffusion, subdiffusion, confined diffusion and directed/active motion by a random forest approach (through Renjin).
ilastik
A simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi-automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode.
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