hundlab-AFAT 1.0

Automated Fibrosis Analysis Toolkit: A tool to quantify the amount of fibrosis in Masson’s Trichrome stains

Automated Fibrosis Analysis Toolkit (AFAT)

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

Hundlab Website: hundlab.org

PyPI: pypi.org/project/hundlab-AFAT

Github: github.com/hundlab/MAT

Setup

Windows

1. Python 3 will need to be installed prior to setting up AFAT, 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 AFAT by opening a cmd or powershell window and running py -m pip install hundlab-AFAT, this should install AFAT and all of its dependancies.

3. Once AFAT has been installed it can be run via cmd, powershell or the start menu. To run type AutomatedFibrosisAnalysisToolkit.py. To create a desktop shortcut type AutomatedFibrosisAnalysisToolkit.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 AFAT 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 AutomatedFibrosisAnalysisToolkit.py will be in there. Once the AFAT script has been found, a shortcut can be made to it directly and placed on the desktop.

Note that it may take a few seconds for AFAT to start.

Mac/Linux

1. Python 3 will need to be installed prior to setting up AFAT. Python 3 can be installed via your package manager in linux, or downloaded from python.org for mac. If it is installed correctly opening a terminal and typing python --version (in some distributions such as Ubuntu the command is python3) should start a python prompt. It may also be necessary to install Tkinter. On unbuntu the package is python3-tk.

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

3. To run AFAT use the command AutomatedFibrosisAnalysisToolkit.py

Usage

TODO!! For now see the paper.