napari-cosmos-ts

napari plugin for colocalization single-molecule spectroscopy (CoSMoS) time series (TS) analysis.

• Install
• Run
• Documentation

Install

If you are unfamiliar with how to create a python environment or pip install a package, see the detailed installation instructions below.

Requires napari.

pip install "napari[all]"

Install latest release version:

pip install napari-cosmos-ts

Or install latest development version:

pip install napari-cosmos-ts@git+https://github.com/marcel-goldschen-ohm/napari-cosmos-ts

To upgrade a previously installed version, simply add the --upgrade flag to the above install commands.

Run

Launch the napari viewer. In a command shell or terminal where you have activated the virtual environment where you installed napari-cosmos-ts run the following command:

napari

Launch the napari-cosmos-ts plugin: From the napari viewer Plugins menu select Colocalization Single-Molecule Time Series (napari-cosmos-ts). This should bring up the napari-cosmos-ts docked widget within the viewer.

Documentation

:construction:

Install for Beginners

1. Install the conda package manager. Simplest is to download Miniconda and run the installer.
2. Create a virtual python environment named napari-env (or name it whatever you want) in which to install napari and this plugin. In a command shell or terminal run the following command:

conda create --name napari-env python

3. Activate your virtual environment. !!! Note you will have to do this every time you open a new command shell or terminal. In a command shell or terminal run the following command:

conda activate napari-env

4. Install napari into your virtual environment. In a command shell or terminal where you have activated your virtual environment run the following command:

pip install "napari[all]"

5. Install napari-cosmos-ts into your virtual environment. In a command shell or terminal where you have activated your virtual environment run the following command:

pip install napari-cosmos-ts

Or for the latest version of napari-cosmos-ts:

pip install napari-cosmos-ts@git+https://github.com/marcel-goldschen-ohm/napari-cosmos-ts

!!! Remember, every time you open a new command shell or terminal you will need to activate the virtual environment where you installed napari-cosmos-ts before running the app.