QSIM: Quantitative structured illumination microscopy image processing in ImageJ

Liang Gao

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish (US)
Article number4
JournalBioMedical Engineering Online
Issue number1
StatePublished - Jan 14 2015


  • 3D imaging
  • ImageJ
  • Quantitative imaging
  • Structured illumination microscopy

ASJC Scopus subject areas

  • Radiological and Ultrasound Technology
  • Biomaterials
  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging


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