SPIT

Single Particle Interaction Tracking (SPIT) is a Python library for single-molecule experiments. The modules in this library can be used to localize particles from a raw movie, link their movements across frames into trajectories, and run analyses on trajectories to detect local colocalization and interaction.

Installation

1. Install Anaconda and git. Open Anaconda prompt.
2. git clone https://github.com/jungmannlab/picasso
3. cd .. into parent folder, git clone https://github.com/GanzingerLab/SPIT
4. cd SPIT and create environment conda env create -f=environment.yml
5. activate environment with activate SPIT
6. build package: cd .. and cd picasso to move to picasso repository and python setup.py install
7. build package: cd .. and cd SPIT to move to SPIT repository and python setup.py install (or use python setup.py develop in case you want to work on the code)

Usage

SPIT is executable from the command line. The following modules can be either executed individually, or consecutively:

Localize - localizes particles in frames
Link - links localizations into trajectories
Colocalize - checks for interactions between trajectories
FRAP - performs a FRAP analysis of a SLB

Contributions

Christian Niederauer
Miles Wang-Henderson
Elia Escoffier

Citing SPIT