WIS-PhagoTracker

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 the Weizmann 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.

References:

[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.

Download:

Please note that this download page is intended only for academic research .

For a download password, please e-mail benny.geiger@weizmann.ac.il. When applying for a password, please make sure to include your name and institute name .

Download software (zip file). The zip file includes WIS-PhagoTracker executable together with few images that will enable you to test it. Check documentation for installation instruction.

Download Documentation (PDF).

WIS-PhagoTracker is a compiled Matlab application. To use it, you should download and install the proper version of Matlab Runtime Component (MCR)
on your computer: MCRInstaller for Win 32bit or MCRInstaller for Win 64bit.
In addition you should also install MCRInstaller 7.13. which is needed by the underlying segmentation program.

WIS-PhagoTracker can handle well montage and whole plates using the MRC (.r6d) format. If you have your montage in tif format, you can break the montage into single FOVs and pack them into MRC file using the Montage2MRC utility. If you have your files as single FOVs and you want to create a montage and pack them into MRC file you can use the PackWellMontage utility. Both utilities can be downloaded from MRC utilities. These are compiled Matlab applications and need the proper MCRInstaller (either Win 32bit or Win 64bit above).

If you have any question please contact the WIS-PhagoTracker team at ofra.golani@weizmann.ac.il.

News:

Sunday, November 27, 2011

Updated version: 2.3.13, Bug fixed in Updating Statistics Files after Manual Editing.

Monday, October 24, 2011

Updated version: 2.3.12, supports both Win 32bit and Win 64bit.

You need to install the proper MCRInstaller from this website, as the Matlab version was upgraded to 2010b.

Thursday, November 4, 2010

Updated version: 2.3.10.

You need to reinstall MCRInstaller from this website, as the Matlab version was upgraded to 2010a.

Wednesday, October 7, 2009

WIS-PhagoTracker was released to the public.