Introduction

SPARTAN allows to extract dual-color particle libraries from large high-throughput SMLM datasets by performing the following steps:

General Workflow

1. Channel registration using 1) a local weighted mean (LWM) and 2) a rigid linear translation
2. Particle segmentation using the wide field fluorescence image
3. Particle filtering and image generation

SPARTAN is further equipped with a number of particle-processing functions as well as an interface into Scipion, an image processing package that allows 3D reconstruction.

General Information

• For pseudocode and processing instructions, see Documentation.

To generate a 3D reconstruction from the input 2D particle library, follow the instructions provided in SPR from SMLM in Scipion.

• The code was developed and tested in MATLAB2016b for Windows 10 and macOS 10.12.6 and requires no non-standard hardware.

Demo

Test Datasets are available in the example data folder as well as at https://doi.org/10.5281/zenodo.1127010

Dependencies

1. To detect the beads within Calculate_AffineT_from_Beads.m, we use parts of a the Matlab Particle Tracking Code repository.

2. For DBSCAN, within particle_filter.m, we use an implementation from Michal Daszykowski

3. Within particle_filter.m, during the calculation of the shape descriptors, we use the code fit_ellipse.m

4. We further make use of the code for efficient subpixel image registration by cross-correlation