Virus

Estimate the frequency of hepatitis C virus infected cells based on the intensity of viral antigen associated immunofluorescence. 

The core is an ImageJ Macro, so it's easy to modify for one's own needs (Link to the code). 

These two similar KNIME workflow solutions take 3D data stacks to segment the spots first, using local thresholding with subsequent morphological operations in order to remove noise. Colocalization is then defined by overlapping or center point distance between segmented objects. Further filtering such as overlapping ratio or distance range is done through KNIME table processing.

Two different types are available. 

1. colocalization based on overlapping
2. colocalization based on distance between object centers

Sample images: Smapp_Ori files

Chapter 4 in the documentation. 

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

This plugin can be used for inferring spatial interactions between patterns of spot-like objects in images or between coordinates read from a file.