A tool that facilitates analyses of data extracted from microscope images of cells
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ContextExplorer facilitates analyses and visualization of data extracted from microscope images of cells.
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.
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 (
ContextExplorer can be installed via the package managers
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:
- Open the
Anaconda Navigatorby searching for it in the start menu.
- Click the
Channelsbutton and add "joelostblom" as a new channel.
- Use the navigation pane on the left to switch to the
- Change the dropdown meny from "installed" to "all" to see packages not yet installed on your system.
- Search for "context-explorer"
- Click the checkbox on the left and select "Mark for installation".
Applyin the bottom right corner and click through the dialog to install
- To run the program, open the
Anaconda Promptfrom the start menu (or the terminal on OS X and Linux), type in
ctexplorerand hit enter.
- If you are using Windows, open up the
Anaconda Promptfrom the start menu. On MacOS and Linux you can use your default terminal (e.g.
terminal.appon MacOS) instead of the
conda install -c joelostblom context_explorerand press enter.
- After the installation has finished, run the program by typing
ctexplorerand hitting enter.
Click the same checkbox as during installation and select "Mark for update", then hit apply in the bottom right corner.
conda update context_explorer
If you are new to ContextExplorer, first download the sample
(right click link -> Save as). Launch ContextExplorer 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
Detailed documentation and workflow examples are available at the documentation page.
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.
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
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