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Welcome to the macrosight wiki!

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.

Quick start - Installation

To clone this repository use the following command:

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

This will not have all functionalities, as @phagosight is necessary to run it.

Installation with phagosight

You need to clone PhagoSight as "recursive", which will pull macrosight as a submodule.

git clone --recursive https://github.com/alonsoJASL/phagosight/

At the moment, you will be pulling my fork of the original @phagosight.

To configure the paths automatically, inside Matlab Run the command configureMacrosight.

Requirements of the data

The macrophages dataset need to be in individual files, with the following naming convention:

/path/to/data/MACROSN/T000ix.tif

where N corresponds to the nth experiment and ix correspond to each image's identifier.

Functionalities will soon be included to prepare the data automatically.

Quick start guide

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 in the initialisation file: initscript.m. The file allows the user to select an experiment and continue on a previously loaded dataset.

Troubleshooting and questions

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

Log files

The log files kept for this package are not written for a full explanation, but rather as a way to keep track of the developments made. So if there is some problem with it, just ask me! The log files can be read in the following order:

• Shape analysis log
• Single cell following log, a previous step from shape evolution.
• Shape evolution CURRENTLY under development. Some of the images present can be hard to see, but the MATLAB fig or EPS files are present in the figs folder.
• (Original development, then switched approach to shape evolution) SOM shape evolution log. This is not finalised.

Also, please notice that this research is ongoing, so bugs are likely to appear. Some of the functions might not be present, because they are part of another package that has not been uploaded. If you are thinking of using our code, please feel free to submit any issues to the issues page, so that small bugs are dealt with.