bmmltools 0.2.4

BioMaterial Machine Learning tools (bmmltools), package to do machine learning with large binary 3d images

bmmltools

Current version 0.2.4

Last update 20/10/2022

PyPI: https://pypi.org/project/bmmltools/

Documentation: https://bmmltools.readthedocs.io/en/latest/

Author: Curcuraci L.

Contacts: [e-mail]

This is a python library for 3d binary image segmentation developed at Max-Plank-Institute fuer Kolloid-und Grenzflaechenforschung. This library contains a series of tools which can be useful to segment 3d binary images based on their structural/texture properties and extract information from the various regions identified,

Installation

To install bmmltools use the Anaconda propt. In the propt, copy the lines below

> (base) conda create -n new_env python=3.8
> (base) conda activate new_env
> (new_env) conda install pytables=3.6.1
> (new_env) conda install hdbscan
> (new_env) pip install bmmltools

Result visualization: bmmlboard

To inspect the intermediate results, a series of standard visualization tools has been developed. They are collected in the bmmlboard, which is a web-browser based a graphical interface, which can be used to visualize the intermediate results of bmmltools. To run the bmmlboard, write in the anaconda prompt

> (base) conda activate new_env
> (new_env) python -m bmmltools.run_bmmlboard

assuming that bmmltools is installed in the "new_env" environment.

Example usage

A series of example scripts are available in the 'example folder' of this repository. A detailed explanation of what they do can be founs in the "Miscellaneous" section of the bmmmltools documentation.