Package: maphis
MAPHISMAPHIS is a GPL open-source application that allows you to automatically or manually perform hierarchical segmentation of arthropod photos, and to extract various measurements describing the size, shape, colour, or texture properties of their individual body parts.The application is not limited only to arthropod photos. With a different segmentation plugin or using manual editing, even photos from completely unrelated domains can be processed.Below you will find instructions how to obtain and installMAPHIS. Please visithttps://maphis.fi.muni.cz/for more resources aboutMAPHIS.Installing and running on WindowsFor Windows users we provide a convenient distribution package at:https://cbia.fi.muni.cz/files/software/maphis/maphis.zip.
Extract the contents of the downloaded zip-file at a destination of your choosing and runMAPHISby executing the filemaphis.exeinside the extracted folder.NOTE: This way of obtaining and runningMAPHISis the most convenient. However, because of the way the distribution is generated, you may encounter thatMAPHISfreezes when clicking on labels in theLabelstree view (it does not happen on all machines, though). As far as we know this problem is notMAPHIS-specific and is currently out of our hands, and therefore if you do encounter such a problem, we recommend looking at the alternative ways of installingMAPHISdetailed in the sections below.Alternative ways of installingMAPHISThe next two sections detail how to installMAPHISeither through thePython Package Indexorgit. The required prerequisite for both of these ways is to have thePythoninterpreter installed. You can obtainPythonfromhttps://www.python.org/.MAPHISis compatible withPythonversions3.8or later, however it was developed and extensively tested mainly withPython 3.8.Virtual environmentAsMAPHIScontains a few dependencies, their versions might clash with versions of the same dependencies that you already may have installed in yourPython environment. To prevent this, we recommend installingMAPHIS(and it is generally a good practice for other big projects) in its ownvirtual environment(seehttps://realpython.com/python-virtual-environments-a-primer/#why-do-you-need-virtual-environmentsfor further explanation).The steps below describe how to create a virtual environment using theminicondamanager. Virtual environment management can be also achieved with the modulesvenv(https://docs.python.org/3/library/venv.html) orvirtualenv(https://virtualenv.pypa.io/en/latest/).Download and installminicondafor your operating system fromhttps://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html.Open upAnaconda Powershell PromptorAnaconda Prompt(Windows) or your terminal emulator (Linux).In the prompt, create a new virtual environment calledmaphiswith Python 3.8 (you can change the version inpython=3.8as you like, it should be 3.8 or higher, though):conda create -n maphis python=3.8Alternative 1: Installing from PyPI and running from command line (Linux, Windows)In this section we describe how to obtainMAPHISfrom thePython Package Index(PyPI).InstallationActivate the virtual environment:conda activate maphisInstall the app:python -m pip install maphisRunningActivate the virtual environment:conda activate maphisStartMAPHISlike so:python -m maphisAlternative 2: For developers - cloning thegitrepositoryInstallationClone the repository fromhttps://gitlab.fi.muni.cz/cbia/maphisGo to the root directory of the cloned repositoryActivate the virtual environment:conda activate maphisInstall the requirements:python -m pip install -r requirements.txtInstall the app in editable mode:python -m pip install -e .RunningActivate the virtual environment:conda activate maphisGo to the root directory of the cloned repositoryRun:python maphis/__main__.pyOr you can alternatively runMAPHISwithpython -m maphisafterStep 1.