Phagosight

Tracking Algorithms for Phagocytes and other moving objects.

Installation

After cloning the repository, it is important to add it (with subfolders) to the Matlab path. Full manual and instructions can be found here.

Usage and Quick Start

Phagosight can be used with the help of a GUI that allows the user to select manually the folder where the data is in. This is done by the command

[handles] = neutrophilAnalysis();

The program can be fully automatic, the user knows some or all the parameters. An example of this:

[handles] = neutrophilAnalysis('/path/to/data/', 0, [], [0.2 0.4]);

where parameters not known, or that want to be taken by default, are simply set to empty arrays []. For a detailed review of the input parameters, the help command outputs all the information the user might need.

help neutrophilAnalysis

User Manual

For a detailed and comprehensive user manual, check the Wiki (https://github.com/phagosight/phagosight/wiki) section.

Output and results

Phagosight returns variable handles, which contains information about the tracks and locations where results from intermediate steps are stored. For example, if the path to data is a folder with name Data/, then the new folders created:

• Data_mat_Or Stores the original data in Matlab's own .mat format.
• Data_mat_Re Stores the data after preprocessing, whether it is reduction by subsampling or filtering (if size is not reduced)
• Data_mat_La Stores the labelled data after segmentation.

Citation

Phagosight is released under the GNU General Public License v3. Please cite Phagosight in your publications if it helps your research:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072636

@article{Henry2013,
 author = {Henry, Katherine and Pase, Luke and Ramos-Lopez, Carlos Fernando and
 Lieschke, Graham J. and Renshaw, Stephen A. and Reyes-Aldasoro, Constantino Carlos},
 issn = {19326203},
 journal = {PLOS ONE},
 month = {January},
 number = {8},
 pages = {e72636},
 pmid = {24023630},
 title = {{PhagoSight: An Open-Source MATLAB\textsuperscript{\textregistered}\
 Package for the Analysis of
 Fluorescent Neutrophil and Macrophage Migration in a Zebrafish Model}},
 volume = {8},
 year = {2013}
}