Context aware analysis of cell fate acquisitions
pip install context-explorer==1.2.0
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 facilitates analyses and visualization of data extracted from microscope images of cells.
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.
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
)
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
by searching for it in the start menu.Channels
button and add "joelostblom" as a new channel.Environments
tab.Apply
in the bottom right corner and click through the dialog to
install context-explorer
.Anaconda Prompt
from the start menu (or the
terminal on OS X and Linux), type in ctexplorer
and hit enter.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
.conda install -c joelostblom context-explorer
and press enter.ctexplorer
and hitting enter.conda
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 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.
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.
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.
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
.
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.