Automated Fibrosis Analysis Toolkit: A tool to quantify the amount of fibrosis in Masson’s Trichrome stains
Project description
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
-
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. -
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. -
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 typeAutomatedFibrosisAnalysisToolkit.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 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 theAutomatedFibrosisAnalysisToolkit.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
-
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 ispython3
) should start a python prompt. It may also be necessary to install Tkinter. On unbuntu the package ispython3-tk
. -
Install AFAT using pip:
python -m pip install hundlab-AFAT
-
To run AFAT use the command
AutomatedFibrosisAnalysisToolkit.py
Usage
TODO!! For now see the paper.
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