LookUpSTORM is a 3D real-time single molecule localization microscopy (SMLM) fitting algorithm that uses lookup tables for subpixel single emitter signal fitting.
This is an example implementation for ImageJ 1.x.
Release ImageJ Plugin Version 0.1.2 for ImageJ 1.x (including dependencies)
- Window x64 link to download
- Linux x64 link to download
Unpack the downloaded archive and copy the directories lib (containing LookUpSTORM_CPPDLL.dll or libLookUpSTORM_CPPDLL.so in their respective subdirectories win64 and linux64) and plugins into your ImageJ installation directory (e.g. C:/ImageJ). Now, the plugin LookUpSTORM_-0.1.2-jar-with-dependencies.jar should be in the subdirectory plugins (e.g. C:/ImageJ/plugins).
The plugin can be access from ImageJ within the menu Plugins -> LookUpSTORM -> Analyse Experiment. Load a 16-bit grayscale experiment and generate a lookup table for analysis. Don't forget to set the correct values in the Image Setup tab for your loaded image and a threshold (which can be adapted during analysis) in the General Tab. To start the analysis select the loaded image and press the Fit current button in the plugin window. Further detail are described in the wiki.
LookUpSTORM support the usage of calibration files (YAML) created with ThunderSTORM. See wiki for details.
Experimental data for the published paper Real-Time 3D Single-Molecule Localization Microscopy Analysis Using Lookup Tables:
- Fig 1: link to download (see details)
- Fig 2: link to download (see details)
- Fig 3: link to download (see details)
Please cite our paper Real-Time 3D Single-Molecule Localization Microscopy Analysis Using Lookup Tables, Vol. 12, Issue 8, pp. 4955-4968 (2021) (DOI: 10.1364/BOE.424016)
Library for c++/java can be build using the CMake build system. It is recommended to use the CMake GUI.
In order to build the library for java set the CATCH variable JNI_EXPORT to true.
Other options for building are to use Intel MKL instead of the default minimal ATLAS that is included in the source. Furthermore, to speed up fitting, the CATCH variable USE_AVX_INTRINSIC can be selected (it is automatically checked if the system provides AVX2).
- Windows 10 and Ubuntu 20.04.1
- Visual Studio 2019
- Java 1.8 + Maven 14.0.0 in NetBeans IDE 8.2
- ImageJ 1.53h
- CMake 3.18.1