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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 scientist without previous programming experience to quantify these variables, although it is relevant for many research areas. Facilitating this type of analyses can help scientist around the world to improve their understanding of cellular behavior and accelerate their research.

## 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.

## Using ContextExplorer

### Installation

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.

### 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)

Detailed documentation and workflow examples are available at the [documentation page](http://contextexplorer.readthedocs.io/en/latest/).

## 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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