Metadata-Version: 2.1
Name: context-explorer
Version: 1.4.3
Summary: Context aware analysis of cell fate acquisitions
Home-page: https://gitlab.com/stemcellbioengineering/context-explorer
Author: Joel Ostblom
Author-email: joel.ostblom@gmail.com
License: BSD-3
Description: Thanks for stopping by! `（ ^_^）o自自o（^_^ ）`
        
        **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
        
        ![Workflow overview](doc/img/fig1-overview.png)
        
        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](https://www.anaconda.com/download/) (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](https://gitlab.com/stemcellbioengineering/context-explorer/raw/master/sample-data/ce-sample.csv)
        (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](http://contextexplorer.readthedocs.io/en/latest/).
        There is also [a brief video tutorial](https://vimeo.com/295958949) of how to
        use the software.
        
        ## 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).
        
        ## 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](https://stackoverflow.com/questions/46999695/class-fifindersyncextensionhost-is-implemented-in-both-warning-in-xcode-si)
        and [here](https://github.com/lionheart/openradar-mirror/issues/17659). It shows
        up because CE uses the Qt file dialog to pick the input file.
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
