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A tool that facilitates analyses of data extracted from microscope images of cells

Project 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.

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