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README.md

SMAP

Superresolution microscopy analysis platform

COPYRIGHT: Jonas Ries, 2020 LICENSE: GPLv3 AUTHOR: Jonas Ries, EMBL Heidelberg, ries@embl.de 27.03.2020 www.rieslab.de, www.github.com/jries/SMAP PLEASE CITE AS: Ries, J. SMAP: a modular super-resolution microscopy analysis platform for SMLM data. Nat Methods (2020). https://doi.org/10.1038/s41592-020-0938-1 Please also cite the references for the plugins you use (as mentioned in the plugin info).

Documentation and installation instructions at: /Documents/Manual/SMAPStep-by-StepGuide.md Instructions for using SMAP to analyze nuclear pore complex standard samples: /Documentation/Manual/SMAP_manual_NPC.pdf

Please cite as: Ries, J. SMAP: a modular super-resolution microscopy analysis platform for SMLM data. Nature Methods (2020) doi:10.1038/s41592-020-0938-1.

Requirements

  1. MATLAB 2019a and newer. Toolboxes: Optimization, Image processing, Curve fitting, Statistics and Machine Learning. A fully funcrtional stand-alone version that does not require a MATLAB license but is limited in extendability can be downloaded at www.rieslab.de.

  2. Mac or Windows

  3. For GPU fitting: Windows, NVIDIA graphics card. CUDA driver (recommended: version 7.5). All fitters also come with a CPU version that is used when these specifications are not met.

Installation

  1. Clone git repository:

    a. Use Terminal (MacOS) or Cmd (Win). Use cd to navigate to the target directory. (e.g. cd git)

    b. Type: git clone https://github.com/jries/SMAP and type in your username and password for your git account.

    c. Install the 3D fitter by typing

git clone https://github.com/jries/fit3Dcspline

  1. Install Micromanager 1.4.22 from https://micro-manager.org

  2. If needed install www.openmicroscopy.org/bio-formats/downloads

  3. In Matlab: run SMAP.m, if questioned, change folder.

  4. In the Menu select SMAP/Preferences... Switch to the Directories tab and select the directories of Micro-Manager and of the bioformats_package.jar. Press Save and exit.

Typical install times: 15 minutes.

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