Computational protocol: The Ordered Extension of Pseudopodia by Amoeboid Cells in the Absence of External Cues

Similar protocols

Protocol publication

[…] Images were analyzed using ImageJ (http://rsb.info.nih.gov/ij/) with a custom made macro that provides a semi-automatic method to characterize pseudopodia. The investigator identifies the start and final position of a pseudopod growth. The macro exports the frame number and x,y-coordinates of these positions, and prints a hard-copy arrow on the relevant frames of the movie. [...] The automated pseudopod tracking algorithm Quimp3 is a macro for the open source program ImageJ (http://rsb.info.nih.gov/ij/) and is written as an extension of the Quimp2 program . The package can be downloaded from the site that also contains the previous versions of Quimp: http://www2.warwick.ac.uk/fac/sci/systemsbiology/staff/bretschneider/quimp. A detailed description of Quimp3 is presented in and in the help file of the package.The phase contrast movie was converted to a black and white movie using the “phase contrast to BW” macro that is included in the Quimp3 package. Some manual adjustment was required to close a few gaps in the cell silhouette. The resulting file was used as input file for the Quimp3 analysis. The pseudopodia were detected using the default parameters of the macro. The Quimp3 produces a data result containing quantitative data for each pseudopod such as the x,y,t coordinates at start and end of the growing phase, the surface area (µm2), area change (µm2/s), and qualitative data such as the assignment of split versus de novo. The pseudopodia can be drawn on top of the contours of the cell, using colour codes for the different pseudopod types (see ). […]

Pipeline specifications

Software tools ImageJ, Quimp
Application Microscopic phenotype analysis