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ijlookupstorm

ImageJ 1.x implementation of a 3D real-time single molecule localization microscopy algorithm based on lookup tables

https://github.com/curtlab/ijlookupstorm

Science Score: 57.0%

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    Found 3 DOI reference(s) in README
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    Low similarity (12.0%) to scientific vocabulary

Keywords

fitting-algorithm lookup-table microscopy smlm
Last synced: 6 months ago · JSON representation ·

Repository

ImageJ 1.x implementation of a 3D real-time single molecule localization microscopy algorithm based on lookup tables

Basic Info
  • Host: GitHub
  • Owner: CURTLab
  • License: mit
  • Language: C
  • Default Branch: master
  • Homepage:
  • Size: 504 KB
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 1
Topics
fitting-algorithm lookup-table microscopy smlm
Created about 5 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.md

LookUpSTORM

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.

Thumbnail

Release

Release ImageJ Plugin Version 0.1.2 for ImageJ 1.x (including dependencies) * Window x64 link to download * Linux x64 link to download

Installation

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).

Run Plugin

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.

Using own experiments

LookUpSTORM support the usage of calibration files (YAML) created with ThunderSTORM. See wiki for details.

Data

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)

Citation

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)

Building Library

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).

Tested prerequisites for compilation

  • 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

Owner

  • Login: CURTLab
  • Kind: user
  • Location: Linz, Austria

Citation (CITATION.cff) 

cff-version: 1.2.0
message: "If you use this work in your research, please cite the following article:"
title: "Real-Time 3D Single-Molecule Localization Microscopy Analysis Using Lookup Tables"
authors:
  - family-names: "Hauser"
    given-names: "Fabian"
    orcid: "https://orcid.org/0000-0002-0992-0861"
  - family-names: "Jacak"
    given-names: "Jaroslaw"
    orcid: "https://orcid.org/0000-0002-4989-1276"
version: "0.1.2"
doi: 10.1364/BOE.424016
date-released: 2021-07-16
url: "https://github.com/CURTLab/IJLookUpSTORM"
preferred-citation:
  type: article
  authors:
  - family-names: "Hauser"
    given-names: "Fabian"
    orcid: "https://orcid.org/0000-0002-0992-0861"
  - family-names: "Jacak"
    given-names: "Jaroslaw"
    orcid: "https://orcid.org/0000-0002-4989-1276"
  journal: "Biomedical Optics Express"
  start: 4955
  end: 4968
  title: "Real-Time 3D Single-Molecule Localization Microscopy Analysis Using Lookup Tables"
  volume: 12
  issue: 8
  year: 2021
  doi: "10.1364/BOE.424016"

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Dependencies

pom.xml maven
  • net.imagej:ij provided
  • org.apache.commons:commons-math3