macrosight

A MATLAB package for the analysis of overlapping macrophages

This code is based on the phagosight software, but modules for the analysis of overlapping cells within a video sequence have been added. For more detailed explanations, developer logs and explanations of routines, we are building a wiki.

Installation

To clone this repository use the following command:

git clone https://github.com/alonsoJASL/macrosight/

To configure the paths automatically, inside Matlab, run the command configureMacrosight. If you have @phagosight, then the configuration will walk you through adding it to your path. Otherwise, you can choose not to use it.

Quick start

The best way to see Macrosight's functionalities is through the demos. In Matlab run

macrosight_demo

to get a list of ready-made examples of the software functionalities:

macrosight_demo
[MACROSIGHT_DEMOS] Select the demo from the list:
[1] Select contact events - save to xls.
[2] Load from saved data - plot results
[3] Load from saved data - statistical analysis
[9] Demo tidy function
[C] Cancel
Your choice [default=1]:

Quick start using phagosight functionalies (from scratch)

Tracking needs PhagoSight, clone it with the command:

git clone https://github.com/phagosight/phagosight/

and then in Matlab run configureMacrosight.

Macrosight takes images stored in a hard drive, and saves the output to other folders following a specific naming scheme. For segmentation, see the file preinit_segmentation.m. This script arranges the data into the cooresponding output folders

• _data_Ha
• _data_Re
• _data_La

Tracking and inclusion of clump information, is done with the setup function: setupInitialStructures.m. The function allows the user to select an experiment and continue on a previously loaded dataset.

[tablenet, clumptracktable, clumpidcodes, ~] = setupInitialStructures();

Troubleshooting and questions

Macrosight is an ongoing project at an early stage. We welcome all feedback and comments in the issues page.