napari-cosmos-ts

napari-cosmos-ts

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

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

  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
  1. 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
  1. 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]"
  1. 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
  1. Activate your virtual environment (see Install, replace napari-env with the name of your environment). In a command shell or terminal run the following command:
conda activate napari-env
  1. Update napari-cosmos-ts in 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 --update

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

pip install napari-cosmos-ts@git+https://github.com/marcel-goldschen-ohm/napari-cosmos-ts --update
  1. Activate your virtual environment (see Install, replace napari-env with the name of your environment). In a command shell or terminal run the following command:
conda activate napari-env
  1. Launch the napari viewer. In a command shell or terminal where you have activated your virtual environment run the following command:
napari
  1. 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 a docked widget within the viewer. Now you are good to go!

:construction:

Version:

  • 0.1.8

Last updated:

  • 08 June 2024

First released:

  • 11 April 2024

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 1
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

  • Information not submitted

Requirements:

  • napari>=0.4.19.post1
  • pyqtgraph>=0.13.4
  • pystackreg>=0.2.7
  • pycpd>=2.0.0
  • qtawesome>=1.3.1