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        "description": "Thanks for stopping by! `\uff08 ^_^\uff09o\u81ea\u81eao\uff08^_^ \uff09`\n\n**Note** The package installation name has changed to `context-explorer`\n(hyphen) and the command to run the program is now `ctexplorer`. Previously\nboth of these were `context_explorer` (underline).\n\n# Context-explorer\n\nContext-explorer facilitates analyses and visualization of data extracted from\nmicroscope images of cells.\n\n## Relevance\n\nThe analyses methods in Context-explorer focuses on how populations of cells\nare affected by their microenvironment, including local variations in cell\nsignalling and cell density. It is currently difficult for scientists without\nprevious programming experience to quantify these variables, although it is\nrelevant for many research areas. Facilitating this type of analyses can help\nscientists around the world to improve their understanding of cellular behavior\nand accelerate their research.\n\n## Overview\n\n![Workflow overview](doc/img/fig1-overview.png)\n\nContext-explorer is controlled via a graphical user interface and aims to\nenable powerful analysis and visualizations of single cell data extracted from\nmicroscope images for a broad scientific audience. Context-explorer can work in\ntandem with many other tools since it only depends on a correctly formatted\nCSV-file as input and only outputs commonly used file formats (`.csv`, `.jpg`,\n`.png`, and `.pdf`)\n\n\n## Installation\n\nContext-explorer can be installed via the package managers `conda` or `pip`, or\nvia the source code on GitLab. The recommended way is to use `conda`. To get\nstarted, first download and install the [Anaconda Python\ndistribution](https://www.anaconda.com/download/) (version 3.x). This will\ninstall Python together with common Python packages used for scientific\ncomputing and the `conda` package manager. Proceed to use `conda` from either\nthe graphical program `Anaconda Navigator` or the command line:\n\n### Anaconda Navigator\n\n1. Open the `Anaconda Navigator` by searching for it in the start menu.\n2. Click the `Channels` button and add \"joelostblom\" as a new channel.\n3. Use the navigation pane on the left to switch to the `Environments` tab.\n4. Change the dropdown meny from \"installed\" to \"all\" to see packages not yet\n   installed on your system.\n5. Search for \"context-explorer\"\n6. Click the checkbox on the left and select \"Mark for installation\".\n7. Hit `Apply` in the bottom right corner and click through the dialog to\n   install `context-explorer`.\n8. To run the program, open the `Anaconda Prompt` from the start menu (or the\n   terminal on OS X and Linux), type in `ctexplorer` and hit enter.\n\n\n### Command line\n\n1. If you are using Windows, open up the `Anaconda Prompt` from the start menu.\n   On MacOS and Linux you can use your default terminal (e.g. `terminal.app` on\n   MacOS) instead of the `Anaconda Prompt`.\n2. Type `conda install -c joelostblom context-explorer` and press enter.\n3. After the installation has finished, run the program by typing `ctexplorer`\n   and hitting enter.\n\n### Updates using `conda`\n\n#### Anaconda Navigator\n\nClick the same checkbox as during installation and select \"Mark for update\",\nthen hit apply in the bottom right corner.\n\n#### Command line\n\n`conda update context-explorer`\n\n## Using Context-explorer\n\nIf you are new to context-explorer, first download [the sample\ndata](https://gitlab.com/stemcellbioengineering/context-explorer/raw/master/sample-data/ce-sample.csv)\n(right click link -> Save as). Launch context-explorer by typing `ctexplorer`\nin the terminal/`Anaconda Prompt`, then choose the sample file (or your own\ndata) from the file selector. That's all you need to start testing\ncontext-explorer!\n\nKeep an eye on the terminal window for the output messages from\ncontext-explorer. Detailed documentation and workflow examples are available at\nthe [documentation page](http://contextexplorer.readthedocs.io/en/latest/).\nThere is also [a brief video tutorial](https://vimeo.com/295958949) of how to\nuse the software.\n\n## Support\n\nIf you run into troubles, please [check the issue\nlist](https://gitlab.com/stemcellbioengineering/context-explorer/issues) to see\nif your problem has already been reported. If not, open a new issue or [ask for\nhelp in the gitter chat](https://gitter.im/context_explorer/Lobby).\n\n## Contributions\n\nFeedback and suggestions are always welcome! This does not have to be\ncode-related, don't be shy =) Please read [the contributing\nguidelines](https://gitlab.com/joelostblom/context-explorer/blob/master/CONTRIBUTING.md)\nto get started.\n\n## Roadmap\n\nAn overview of the projects direction is available in [the project\nwiki](https://gitlab.com/stemcellbioengineering/context-explorer/wikis/Roadmap).\n\n## Code of conduct\n\nBe welcoming, friendly, and patient; be direct and respectful; understand and\nlearn from disagreement and different perspectives; lead by example; ask for\nhelp when unsure; give people the benefit of the doubt; a simple apology can go\na long way; be considerate in the words that you choose. Detailed descriptions\nof these points can be found in\n[`CODE_OF_CONDUCT.md`](https://gitlab.com/stemcellbioengineering/context-explorer/blob/master/CODE_OF_CONDUCT.md).\n\n## Known issues\n\nError output:\n\n```\nobjc[42840]: Class FIFinderSyncExtensionHost is implemented in both\n/System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit\n(0x7fff9d6a3c90) and\n/System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride\n(0x1c279d2cd8). One of the two will be used. Which one is undefined. ```\n```\n\nSolution:\n\nThis error is unrelated to CE and appears to origin from the Finder software in\nMacOS as discussed\n[here](https://stackoverflow.com/questions/46999695/class-fifindersyncextensionhost-is-implemented-in-both-warning-in-xcode-si)\nand [here](https://github.com/lionheart/openradar-mirror/issues/17659). It shows\nup because CE uses the Qt file dialog to pick the input file.",
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