StormChaser

DEMO: 3D Double-Helix localization software

StormChaser is based on a c++ SM localization routine converted in a exectutable standalone .mex file. Here only the .mex file is provided.

Included: Artifical DH Dataset Generators

Installation

StormChaser uses Matlab R2015 and a few scientific c++ libraries associated with it. To run the DEMO:

• Save all the files in the same directory
• Unzip the file StormChaser.rar
• Open the scrip named StormChaser_DEMO1.m
• Run the scrip following the instructions reported on the head of the StormChaser_DEMO1.m file

License Information

© All rights reserved. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, Laboratory of Experimental Biophysics, 2016-2017

Author

Anna Archetti anna.archetti@gmail.com

Internal Workflow

fRapidDH.m is the main function.

Preliminary steps:

• Parameters definition;
• Find first guess for the seed threshold and the cluster threshold (the cluster thr: intensity value of the possible max peak of a lobe the seed thr: value of intensity of the pixel belonging to a lobe);
• Test the choosen thresholds by checking the file generated by the software with the images with a red cross overlapped to each found lobe or the images with the pixel corresponding to each lobe color with different colors

Main steps:

1. DH-PSF calibration (dhCalibration.m)
2. molecule identification via lobes search (Center of mass approach) and lobes pairing (CM_forDH)
3. first rejection and image segmentation preparetion for step 4) (lobePairRejection.m getParamLocInitGuess.m)
4. molecule localization via LS or MLE multi-emitter fitting (MLElocalization.m)
5. filtering
6. Correction for spherical aberration
7. Intensity Conversion from ADU to photons
8. Result localizations displaying
9. Wobble correction % 10) Result saving