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

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# ContextExplorer

ContextExplorer facilitates analyses and visualization 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

![Workflow overview](doc/img/fig1-overview.png)

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)

## Installation

ContextExplorer can be installed via the package managers conda or pip. The recommended way is to use conda:

  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 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.

## Using ContextExplorer

If you are new to ContextExplorer, first download [the sample data](https://gitlab.com/stemcellbioengineering/context-explorer/raw/master/sample-data/ce-sample.csv) (right click link -> Save as). Launch ContextExplorer by typing context_explorer in the terminal/Anaconda Prompt, then choose the sample 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/).

## Support

If you run into troubles, please [check the issue list](https://gitlab.com/stemcellbioengineering/context-explorer/issues) to see if your problem has already been reported. If not, open a new issue or [ask for help in the gitter chat](https://gitter.im/context_explorer/Lobby).

## Contributions

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.

## Roadmap

An overview of the projects direction is available in [the project wiki](https://gitlab.com/stemcellbioengineering/context-explorer/wikis/Roadmap).

## Code of conduct

Be welcoming, friendly, and patient; be direct and respectful; understand and learn from disagreement and different perspectives; lead by example; ask for help when unsure; give people the benefit of the doubt; a simple apology can go a long way; be considerate in the words that you choose. Detailed descriptions of these points can be found in [CODE_OF_CONDUCT.md](https://gitlab.com/stemcellbioengineering/context-explorer/blob/master/CODE_OF_CONDUCT.md).

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