Macrophage Analysis Toolkit: A tool to quantify macrophage presence
Project description
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
-
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. -
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. -
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 typeMacrophageAnalysisToolkit.py
into the start menu selectCopy full path
, then on the Desktopright-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 theMacrophageAnalysisToolkit.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
-
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 isqt5-default
. -
Install MAT using pip:
python -m pip install hundlab-MAT
-
To run MAT use the command
MacrophageAnalysisToolkit.py
.
Usage
TODO!! For now see the paper.
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