Macrophage Anlaysis Toolkit (MAT)

This tool was documented in our paper on marcophage and fibrosis quantification

Hundlab Website: hundlab.org

PyPI: pypi.org/project/hundlab-MAT

Github: github.com/hundlab/MAT

Setup

Windows

1. Python 3 will need to be installed prior to setting up MAT, preferably any python greater than 3.7. Python 3 can be downloaded from the python website. The x86-64 executable installer is reccommended, as the default install configuration will set python to open .py files by double clicking. If it is installed correctly opening cmd or powershell window and typing py --version will print the installed python version.

2. Install MAT by opening a cmd or powershell window and running py -m pip install hundlab-MAT, this should install MAT and all of its dependancies.

3. Once MAT has been installed it can be run via cmd, powershell or the start menu. To run type MacrophageAnalysisToolkit.py. To create a desktop shortcut type MacrophageAnalysisToolkit.py into the start menu select Copy full path, then on the Desktop right-click -> new -> new shortcut and paste the path when it askes for a path.

   If MAT does not run above as described this means that the python scipts directory has not been added to the windows path. To find the install location of python type py -0p this will give the location of the python executable. In the same directory as python.exe is a Scripts directory and the MacrophageAnalysisToolkit.py will be in there. Once the MAT script has been found, a shortcut can be made to it directly and placed on the desktop.

Note that it may take some time for MAT to start and it may be slow with larger images. On some machines the calibration widgets are especially slow

Mac/Linux

1. Python 3 will need to be installed prior to setting up MAT. Python 3 can be installed via your package manager in linux. If it is installed correctly opening a terminal and typing python --version (in some distributions such as Ubuntu the command is python3) should print the python version. It may also be necessary to install Qt5. On unbuntu the package is qt5-default.

2. Install MAT using pip: python -m pip install hundlab-MAT

3. To run MAT use the command MacrophageAnalysisToolkit.py.

Usage

TODO!! For now see the paper.