ardiloot / smolphot

SMolPhot is an open-source operating system independent data analysis and visualization software package for data acquired by single molecule localization microscopy methods such as photo-activation localization microscopy. SMolPhot is written in python which make it platform independent and easy to develop open source software package.

About

SMolPhot is an open-source operating system independent data analysis and visualization software package for data acquired by single molecule localization microscopy methods such as photo-activation localization microscopy. SMolPhot is written in python which make it platform independent and easy to develop open source software package.

This software is developed by the scientists of University of Tartu (see team) for the Single-Molecule Localization Microscopy Software Challenge 2016 (). For the results of the competition see the local and the .

Main features

• Easy to use: one click installer for most operating systems (Windows, Linux, Mac)
• Pre-processors for noise filtering and background subtraction;
• Uses astigmatism approach as a z-calibration tool for 3D localization;
• Includes local-maxima, blob-detection and connected-component localization algorithms;
• 2D and 3D Gaussian point spread functions for fitting;
• Post-processing which filters molecules according to localization goodness classified by standard deviation of fitting parameters or any linear combinations of them defined by user.
• Applies temporal correlation for enhancing localization accuracy by combining locations of single molecule over multiple frames.

Getting started

• User Manual and getting started: User manual
• Source code: Source
• Downloads: Downloads

Team

• Ardi Loot
• Andreas Valdmann
• Marko Eltermann
• Mihkel Kree
• Martti Pärs