Metadata-Version: 1.2
Name: context-explorer
Version: 0.9.2
Summary: A tool that facilitates analyses of data extracted from
        microscope images of cells
Home-page: https://gitlab.com/stemcellbioengineering/context-explorer
Author: Joel Ostblom
Author-email: joel.ostblom@gmail.com
License: BSD-3
Description-Content-Type: UNKNOWN
Description: # ContextExplorer
        
        Thanks for stopping by! `（ ^_^）o自自o（^_^ ）`
        
        ContextExplorer is a software program that facilitates analyses of data
        extracted from microscope images of cells.
        
        ## Relevance
        
        The analyses methods in ContextExplorer focuses on how populations of cells are
        affected by their microenvironment, including local variations in cell
        signalling and cell density. It is currently difficult for scientists without
        previous programming experience to quantify these variables, although it is
        relevant for many research areas. Facilitating this type of analyses can help
        scientists around the world to improve their understanding of cellular behavior
        and accelerate their research.
        
        ## Overview
        
        ContextExplorer is controlled via a graphical user interface and aims to enable
        powerful analysis and visualizations of single cell data extracted from
        microscope images for a broad scientific audience. ContextExplorer can
        work in tandem with many other tools since it only depends on a correctly
        formatted CSV-file as input and only outputs commonly used file formats (`.csv`,
        `.jpg`, `.png`, and `.pdf`)
        
        ## Getting started with ContextExplorer
        
        ### Installation
        
        ContextExplorer can be installed via the package managers `conda` or `pip`. The
        recommended way is to use `conda`.
        
        #### Conda installation
        
        1. Download and install the [Anaconda Python
           distribution](https://www.anaconda.com/download/) (version 3.x). This is an
           easy way to install Python and gives access to the powerful package manager
           `conda`.
        2. If you are using Windows, open up the `Anaconda Command Prompt` from the start menu.
           On MacOS and Linux you can use your default terminal (e.g. `terminal.app` on
           MacOS).
        3. Type `conda install -c joelostblom context_explorer` and press return.
        
        That's it! You can run the program by typing `context_explorer` into the
        terminal/Anaconda Command Prompt.
        
        ### Usage
        
        To try out ContextExplorer, first download [the sample
        data](https://gitlab.com/stemcellbioengineering/context-explorer/raw/master/sample-data/ce-sample.csv)
        (right click link -> Save as). When you launch the program, choose this file
        (or your own data) from the file selector. That's all you need to start testing
        ContextExplorer!
        
        Detailed documentation and workflow examples are available at the [documentation
        page](http://contextexplorer.readthedocs.io/en/latest/).
        
        <!--
        Currently, the software is distributed as source code only. The required
        dependencies are `python3`, `pandas`, `numpy`, `scikit-learn`, `matplotlib`,
        `shapely`, and `natsort`. A `conda` package will be created shortly to
        facilitate installation.
        -->
        
        ## Contributing
        
        Feedback and suggestions are always welcome! This does not have to be
        code-related, don't be shy =) Please read [the contributing
        guidelines](https://gitlab.com/joelostblom/context-explorer/blob/master/CONTRIBUTING.md)
        to get started.
        
        ## Code of conduct
        
        This project adheres to the [Mozilla participation
        guidelines](https://www.mozilla.org/en-US/about/governance/policies/participation/).
        In brief, be respectful, be direct but professional, be inclusive, understand
        different perspectives, appreciate and accommodate our similarities and
        differences, and lead by example.
        
        
        direct and respectful, discuss underlying technical issues instead
        of personal matters, be understanding and helpful to people with less experience
        or a different perspective.
        
Platform: UNKNOWN
Requires-Python: >=3.6
