time-series

Fully-automated cell tracking of 2D+time or 3D+time images with some parameter tuning

Easy-to-use, computationally efficient, two- and three-dimensional, feature point-tracking tool for the automated detection and analysis of particle trajectories as recorded by video imaging in cell biology. 

The tracking process requires no apriori mathematical modelling of the motion, it is self-initialising, it discriminates spurious detections, and it can handle temporary occlusion as well as particle appearance and disappearance from the image region. 

The plugin is well suited for video imaging in cell biology relying on low-intensity fluorescence microscopy. It allows the user to visualize and analyze the detected particles and found trajectories in various ways:

• Preview and save detected particles for separate analysis
• Global non progressive view on all trajectories
• Focused progressive view on individually selected trajectory
• Focused progressive view on trajectories in an area of interest

It also allows the user to find trajectories from uploaded particles position and information text files and then to plot particles parameters vs. time - along a trajectory

ImarisReader is a set of classes for reading the data stored in ims files. ImarisReader can read the primary image data, as well as the data for segmented objects: Cells, Filaments, Spots and Surfaces.

FLIMfit is an OMERO client-side MATLAB application for fitting and visualising time-resolved FLIM data. It supports key data formats including:

• Becker and Hickl .sdt
• LaVision BioTech .msr
• PicoQuant .bin
• OME-TIFF files;

Several options for curve fitting are available. Results can be saved back in OMERO, which also facilitates working collaboratively on the data analysis.