rapidSTORM manual

Version 3.3

Steve Wolter

Würzburg University
Biophysik & Biotechnologie

Sven Proppert

Würzburg University
Biophysik & Biotechnologie

Sarah Aufmkolk

Würzburg University
Biophysik & Biotechnologie

André Lampe

Freie Universität Berlin
Labor für Membranbiochemie und Molekulare Zellbiologie

Teresa Klein

Würzburg University
Biophysik & Biotechnologie

This document is the official manual of the rapidSTORM software. It is generated deterministically during the build process and can be identified and cited using the version number on the front cover as the edition. Dieses Dokument wurde automatisch erstellt und ist ohne Unterschrift gültig.

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.3 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled "GNU Free Documentation License".

June 22, 2018


Table of Contents

Motivation and scope of rapidSTORM
Help on Help
User interface
Basic use tutorial
Behaviour of input fields
Immediate effects and committing values
Multi-dimensional chaining
Optional values
Selecting input files
The output options tree
The menu bar
Job
User level
Help
Image window
Usage examples
Evaluate 3D data with a bead calibration sample
Evaluate spectral demixing measurement
Input options
rapidSTORM engine options
Output options
Localizations file
Image display
Count localizations
Memory Cache
Slice localization set — Split the input along the time axis to make a movie
Average images
Display progress
Estimate PSF form
Look up 3D via sigma difference
3D PSF width calibration table
Track emissions
Expression filter
Common error messages
Fundamental concepts
Input channels
dSTORM engine
Localization
Fluorophore type
3D fitting
Piecewise cubic model
Z calibration file
Polynomial model
Repeater
PSF model
Two-kernel analysis
Linear drift correction
Bibliography

List of Tables

1. Variable base names for expressions
2. Variable name modifiers for expressions
3. Variable example names for expressions
4. Operators in expressions
5. Example actions

List of Equations

1. Polynomial 3D PSF Width