Phago Kinetic Tracks Analysis Tool

WIS-PhagoTracker is a software application for quantitative analysis of high throughput cell migration assay. The cell migration assay [1] is based on a modified Phagokinetic tracks procedure, in which motile cells "leave their tracks" on a specialized surface. These tracks are visualized using a screening microscope.

WIS-PhagoTracker enables morphometric analysis of such tracks. It uses state of the art multiscale segmentation algorithm [2] for fine detection of tracks and cells boundaries. Following the segmentation step, it quantifies various morphometric parameters for each track, such as track area, perimeter, major and minor axis and solidity. All these measures are calculated for each track in each well of a well plate and saved for further statistical analysis.

WIS-PhagoTracker supports all the analysis phases starting from preprocessing, finding tracks of selected wells or a whole plate, through viewing the results and manually rejecting tracks to statistical analysis of the results. It also supports batch processing of several plates, and analysis of single image files. A user interface enables the user to modify the relevant parameters of the process, according to specific image's requirements. Results are exported into Excel readable files. It runs on Windows XP platforms. Users familiar with other Windows programs will find this software fairly straightforward to use.

WIS-PhagoTracker was developed by Ofra Golani, Meirav Galun and Suha Naffar Abu-Amara in the laboratories of Prof. Benny Geiger and Prof. Ronen Basri at the Department of Molecular Cell Biology and the Department of Computer Science and Applied Mathematics at theWeizmann Institute of Science.

The very accurate tracks detection which is the core of WIS-PhagoTracker is achieved by using multi-scale segmentation algorithm [2] developed by: Ronen Basri, Achi Brandt, Meirav Galun, Yoav Karnieli and Eitan Sharon, at the Department of Computer Science and Applied Mathematics at the Weizmann Institute and patented in [3].

Please credit WIS-PhagoTracker by citing the papers describing its underlying methods [1],[2]. We will appreciate it if you would update us with any publication using the tool.


  1. Naffar-Abu-Amara S, Shay T, Galun M, Cohen N, Isakoff SJ, Kam Z and Geiger B.  Identification of novel pro-migratory, cancer-associated genes using quantitative, microscopy-based screening.  PloS ONE. 2008 Jan 23;3(1): e1457. PDF

  2. E.Sharon, M. Galun, D. Sharon, R.Basri and A. Brandt.  Hierarchy and adaptivity in segmenting visual scenes.  Nature, 442 (7104): 810-813 (2006). PDF

  3. Achi Brandt, Eitan Sharon, and Ronen Basri.   "Method and Apparatus for Data Clustering Including Segmentation and Boundary Detection".  U.S. Patent and Trademark Office Application No. PCT/US01/43991, July, 2003, assigned to Yeda Research and Development Co., Ltd., Nov. 2000.


Migration analysis of cells on bone (by Dr. Ariel Livne)

Link to Matlab files, example data and the README files.

These Matlab scripts provide with tools for reliable analysis of cells migrating on non-glass surfaces (such as bone), which may present low signal to noise ratio and frame drift. These scripts can be applied on movie files that are saved as individual frames, and retrieve the corrected movies as individual frames that can be re-stacked using fiji software. These scripts are similar in function to existing fiji plugins, but provide more sensitive analysis for high background and multiple details.

There are three scripts available in the following links, each link contains a README file with instructions, a folder with trial data and the script that should be opened in MATLAB software.

  1. Correct illumination- corrects for uneven illumination of the background, which is crucial for accurate segmentation and tracking of the cells
    pre-background reduction post-background reduction
    pre-background reduction          post background reduction
  2. Correct image alignment- corrects for stage/sample drift by aligning a chosen feature observed in different frames. Ideal for movies that contain background features which may complicate the standard analysis
    post-alignment pre-alignment
    post- alignment                          pre-alignment
  3. Plot XY over time- takes a set of coordinates (inserted in the form of a two dimensional matrix) and plots the track progression in time
    track result