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Note The package installation name has changed to context-explorer (hyphen) and the command to run the program is now ctexplorer. Previously both of these were context_explorer (underline).

Context-explorer

Context-explorer facilitates analyses and visualization of data extracted from microscope images of cells.

Relevance

The analyses methods in Context-explorer 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

Context-explorer 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. Context-explorer 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

Context-explorer can be installed via the package managers conda or pip, or via the source code on GitLab. The recommended way is to use conda. To get started, first download and install the Anaconda Python distribution (version 3.x). This will install Python together with common Python packages used for scientific computing and the conda package manager. Proceed to use conda from either the graphical program Anaconda Navigator or the command line:

Anaconda Navigator

1. Open the Anaconda Navigator by searching for it in the start menu.
2. Click the Channels button and add "joelostblom" as a new channel.
3. Use the navigation pane on the left to switch to the Environments tab.
4. Change the dropdown meny from "installed" to "all" to see packages not yet installed on your system.
5. Search for "context-explorer"
6. Click the checkbox on the left and select "Mark for installation".
7. Hit Apply in the bottom right corner and click through the dialog to install context-explorer.
8. To run the program, open the Anaconda Prompt from the start menu (or the terminal on OS X and Linux), type in ctexplorer and hit enter.

Command line

1. 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) instead of the Anaconda Prompt.
2. Type conda install -c joelostblom context-explorer and press enter.
3. After the installation has finished, run the program by typing ctexplorer and hitting enter.

Updates using conda

Anaconda Navigator

Click the same checkbox as during installation and select "Mark for update", then hit apply in the bottom right corner.

Command line

conda update context-explorer

Using Context-explorer

If you are new to context-explorer, first download the sample data (right click link -> Save as). Launch context-explorer by typing ctexplorer 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 context-explorer!

Keep an eye on the terminal window for the output messages from context-explorer. Detailed documentation and workflow examples are available at the documentation page. There is also a brief video tutorial of how to use the software.

Support

If you run into troubles, please check the issue list to see if your problem has already been reported. If not, open a new issue or ask for help in the gitter chat.

Contributions

Feedback and suggestions are always welcome! This does not have to be code-related, don't be shy =) Please read the contributing guidelines to get started.

Roadmap

An overview of the projects direction is available in the project wiki.

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.

Known issues

Error output:

objc[42840]: Class FIFinderSyncExtensionHost is implemented in both
/System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit
(0x7fff9d6a3c90) and
/System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride
(0x1c279d2cd8). One of the two will be used. Which one is undefined. ```

Solution:

This error is unrelated to CE and appears to origin from the Finder software in MacOS as discussed here and here. It shows up because CE uses the Qt file dialog to pick the input file.