QSIM: quantitative structured illumination microscopy image processing in ImageJ

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Abstract

Background

Structured illumination microscopy has been extensively used in biological imaging due to its low cost and easy implementation. However, the lack of quantitative imaging capability limits its application in absolute irradiance measurements.

Method

We have developed a quantitative structured illumination microscopy image processing algorithm (QSIM) as a plugin for the widely used ImageJ software. QSIM can work with the raw images acquired by a traditional structured illumination microscope and can quantitatively measure photon numbers, with noise estimates for both wide-field images and sectioned images.

Results and conclusion

We demonstrated the quantitative image processing capability of QSIM by imaging a mouse kidney section in 3D. The results show that QSIM can transform structured illumination microscopy from qualitative to quantitative, which is essential for demanding fluorescence imaging applications.

Electronic supplementary material

The online version of this article (doi:10.1186/1475-925X-14-4) contains supplementary material, which is available to authorized users.

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Most cited references 13

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The adult Drosophila posterior midgut is maintained by pluripotent stem cells.

Benjamin Ohlstein, Allan Spradling (2006)

Vertebrate and invertebrate digestive systems show extensive similarities in their development, cellular makeup and genetic control. The Drosophila midgut is typical: enterocytes make up the majority of the intestinal epithelial monolayer, but are interspersed with hormone-producing enteroendocrine cells. Human (and mouse) intestinal cells are continuously replenished by stem cells, the misregulation of which may underlie some common digestive diseases and cancer. In contrast, stem cells have not been described in the intestines of flies, and Drosophila intestinal cells have been thought to be relatively stable. Here we use lineage labelling to show that adult Drosophila posterior midgut cells are continuously replenished by a distinctive population of intestinal stem cells (ISCs). As in vertebrates, ISCs are multipotent, and Notch signalling is required to produce an appropriate fraction of enteroendocrine cells. Notch is also required for the differentiation of ISC daughter cells, a role that has not been addressed in vertebrates. Unlike previously characterized stem cells, which reside in niches containing a specific partner stromal cell, ISCs adjoin only the basement membrane, differentiated enterocytes and their most recent daughters. The identification of Drosophila intestinal stem cells with striking similarities to their vertebrate counterparts will facilitate the genetic analysis of normal and abnormal intestinal function.

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Accuracy and precision in quantitative fluorescence microscopy

Jennifer C. Waters (2009)

The light microscope has long been used to document the localization of fluorescent molecules in cell biology research. With advances in digital cameras and the discovery and development of genetically encoded fluorophores, there has been a huge increase in the use of fluorescence microscopy to quantify spatial and temporal measurements of fluorescent molecules in biological specimens. Whether simply comparing the relative intensities of two fluorescent specimens, or using advanced techniques like Förster resonance energy transfer (FRET) or fluorescence recovery after photobleaching (FRAP), quantitation of fluorescence requires a thorough understanding of the limitations of and proper use of the different components of the imaging system. Here, I focus on the parameters of digital image acquisition that affect the accuracy and precision of quantitative fluorescence microscopy measurements.

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Method of obtaining optical sectioning by using structured light in a conventional microscope.

M. A. A. Neil, R Juskaitis, T. Wilson (1997)

We describe a simple method of obtaining optical sectioning in a conventional wide-field microscope by projecting a single-spatial-frequency grid pattern onto the object. Images taken at three spatial positions of the grid are processed in real time to produce optically sectioned images that are substantially similar to those obtained with confocal microscopes.

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Author and article information

Contributors

Liang Gao: gaol@wustl.edu

Journal

Journal ID (nlm-ta): Biomed Eng Online

Journal ID (iso-abbrev): Biomed Eng Online

Title: BioMedical Engineering OnLine

Publisher: BioMed Central (London )

ISSN (Electronic): 1475-925X

Publication date (Electronic): 14 January 2015

Publication date Collection: 2015

Volume: 14

Electronic Location Identifier: 4

Affiliations

Department of Biomedical Engineering, Washington University, St. Louis, MO 63139 USA

Article

Publisher ID: 934

DOI: 10.1186/1475-925X-14-4

PMC ID: 4360942

PubMed ID: 25588495

SO-VID: 5eef0790-67e2-42e8-a3d7-bb87e9997e71

License:

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 16 October 2014

Date accepted : 7 January 2015

Custom metadata

ScienceOpen disciplines: Biomedical engineering

Keywords: structured illumination microscopy,quantitative imaging,3d imaging,imagej

Data availability:

ScienceOpen disciplines: Biomedical engineering

Keywords: structured illumination microscopy, quantitative imaging, 3d imaging, imagej

QSIM: quantitative structured illumination microscopy image processing in ImageJ

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Abstract

Background

Method

Results and conclusion

Electronic supplementary material

Related collections

Journal of Disability Research

Most cited references 13

The adult Drosophila posterior midgut is maintained by pluripotent stem cells.

Accuracy and precision in quantitative fluorescence microscopy

Method of obtaining optical sectioning by using structured light in a conventional microscope.

Author and article information

Contributors

Journal

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Article

History

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