Hierarchical segmentation and extraction of various measurements from photos of (not only) arthropods.
Project description
MAPHIS
https://cbia.fi.muni.cz/software/maphis.html
Outline
Prerequisites
MAPHIS is currently compatible only with Python 3.8. In this guide we'll detail how to obtain Python 3.8 and create a Python virtual environment using miniconda (https://docs.conda.io/en/latest/miniconda.html).
Other ways of obtaining Python 3.8 include downloading it from (https://www.python.org/downloads/) or using pyenv (https://github.com/pyenv/pyenv). Virtual environment management can be also achieved with the modules venv (https://docs.python.org/3/library/venv.html) or virtualenv (https://virtualenv.pypa.io/en/latest/).
Set up Python 3.8 and virtual environment
-
Download and install
minicondafor your operating system from: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html -
Open up
Anaconda Powershell PromptorAnaconda Prompt(Windows) or your terminal emulator (Linux/Mac) -
Create a new virtual environment called
maphiswithPython 3.8as its interpreter:conda create -n maphis python=3.8
Installation
Installation from pip
- Activate the virtual environment:
conda activate maphis - Install the app:
python -m pip install maphis
Running
- Activate the virtual environment:
conda activate maphis - Run as:
python -m maphis
Installation from the repository (developer purposes)
- Clone this repository
- Go to the root directory of the cloned repository
- Activate the virtual environment:
conda activate maphis - Install the requirements:
python -m pip install -r requirements.txt - Install the app:
python -m pip install -e .
Running from the repository
- Activate the virtual environment:
conda activate maphis - Go to the root directory of the cloned repository
- Run:
python maphis/__main__.py
User guide
The user guide is located at: https://cbia.fi.muni.cz/software/maphis.html
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