Package: context-explorer
Thanks for stopping by!（ ^_^）o自自o（^_^ ）NoteThe package installation name has changed tocontext-explorer(hyphen) and the command to run the program is nowctexplorer. Previously
both of these werecontext_explorer(underline).Context-explorerContext-explorer facilitates analyses and visualization of data extracted from
microscope images of cells.RelevanceThe 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.OverviewContext-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)InstallationContext-explorer can be installed via the package managerscondaorpip, or
via the source code on GitLab. The recommended way is to useconda. To get
started, first download and install theAnaconda Python
distribution(version 3.x). This will
install Python together with common Python packages used for scientific
computing and thecondapackage manager. Proceed to usecondafrom either
the graphical programAnaconda Navigatoror the command line:Anaconda NavigatorOpen theAnaconda Navigatorby searching for it in the start menu.Click theChannelsbutton and add "joelostblom" as a new channel.Use the navigation pane on the left to switch to theEnvironmentstab.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".HitApplyin the bottom right corner and click through the dialog to
installcontext-explorer.To run the program, open theAnaconda Promptfrom the start menu (or the
terminal on OS X and Linux), type inctexplorerand hit enter.Command lineIf you are using Windows, open up theAnaconda Promptfrom the start menu.
On MacOS and Linux you can use your default terminal (e.g.terminal.appon
MacOS) instead of theAnaconda Prompt.Typeconda install -c joelostblom context-explorerand press enter.After the installation has finished, run the program by typingctexplorerand hitting enter.Updates usingcondaAnaconda NavigatorClick the same checkbox as during installation and select "Mark for update",
then hit apply in the bottom right corner.Command lineconda update context-explorerUsing Context-explorerIf you are new to context-explorer, first downloadthe sample
data(right click link -> Save as). Launch context-explorer by typingctexplorerin 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
thedocumentation page.
There is alsoa brief video tutorialof how to
use the software.SupportIf you run into troubles, pleasecheck the issue
listto see
if your problem has already been reported. If not, open a new issue orask for
help in the gitter chat.ContributionsFeedback and suggestions are always welcome! This does not have to be
code-related, don't be shy =) Please readthe contributing
guidelinesto get started.RoadmapAn overview of the projects direction is available inthe project
wiki.Code of conductBe 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 inCODE_OF_CONDUCT.md.Known issuesError 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 discussedhereandhere. It shows
up because CE uses the Qt file dialog to pick the input file.