cell migration

Implementation of some image correlation spectroscopy tools

The QuimP software from Bretschneider group is deployed as ImageJ plugin and includes model-based cell segmentation, cell outline tracking and quantification of the spatially resolved speed of protrusions and retractions. The algorithm to calculate morphological dynamics is faster compared to other approaches (e.g. Machacek and Danuser, 2006). The reference paper describes the workflow for these analyses.

Requires Matlab Runtime Environment or Matlab. Source code (m-files) are downloaded. Software availability: AVeMap was developed under MATLAB (MathWorks). It is available as an executable, multiplatform program, together with source codes and documentation here, and the source code is also available as Supplementary Software. For practical reasons, this executable version, which does not require MATLAB, runs on a single processor. For users who want to customize the software and/or need the power of parallel computing, an installation of MATLAB with its 'parallel' and 'image processing' toolboxes is needed. Note that, even with the executable version, the velocity fields are stored for further analysis. The add-on AVeMap+ uses these AVeMap-computed velocity fields to generate heat map tables. It is available with the same link.

In this example, cells are grown as a tissue monolayer. Rather than identifying individual cells, this pipeline quantifies the area occupied by the tissue sample.

Download package also contains example images. 

This macro was designed to measure the size of the scratch wound in a wound scratch assay. It uses an edge-detection and thresholding technique.

It will batch process all images in a directory. Images captured by time-lapse should be compiled into stacks using a tool similar to "Metamorph nd & ROI files importer (nd stack builder)" by Fabrice P. Cordelières. Images to be analyzed should be placed in one directory (Source Directory). A second directory should be created to save results files and images (Destination Directory). Setting correct Lower and Upper thresholds is important to obtain a good result. Two macros are available, one using edge detection, the second one using background subtraction.