SMAP

Superresolution microscopy analysis platform

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

Requirements

1. Matlab 2016a or newer. Toolboxes: Optimization, Image processing, Curve fitting, Statistics and Machine Learning. A stand-alone version will be released, but will be limited in extensibility.

2. Mac or Windows

3. For GPU fitting: Windows, NVIDIA graphics card. CUDA driver (recommended: version 7.5).

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

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

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

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

5. 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.