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Zhang Y, Hato T, Dagher PC, Nichols EL, Smith CJ, Dunn KW, Howard SS. Automatic segmentation of intravital fluorescence microscopy images by K-means clustering of FLIM phasors. OPTICS LETTERS 2019; 44:3928-3931. [PMID: 31415514 DOI: 10.1364/ol.44.003928] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/09/2019] [Indexed: 05/18/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) provides additional contrast for fluorophores with overlapping emission spectra. The phasor approach to FLIM greatly reduces the complexity of FLIM analysis and enables a useful image segmentation technique by selecting adjacent phasor points and labeling their corresponding pixels with different colors. This phasor labeling process, however, is empirical and could lead to biased results. In this Letter, we present a novel and unbiased approach to automate the phasor labeling process using an unsupervised machine learning technique, i.e., K-means clustering. In addition, we provide an open-source, user-friendly program that enables users to easily employ the proposed approach. We demonstrate successful image segmentation on 2D and 3D FLIM images of fixed cells and living animals acquired with two different FLIM systems. Finally, we evaluate how different parameters affect the segmentation result and provide a guideline for users to achieve optimal performance.
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Zhang Y, Benirschke D, Abdalsalam O, Howard SS. Generalized stepwise optical saturation enables super-resolution fluorescence lifetime imaging microscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:4077-4093. [PMID: 30615706 PMCID: PMC6157771 DOI: 10.1364/boe.9.004077] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/25/2018] [Accepted: 07/28/2018] [Indexed: 05/29/2023]
Abstract
We present a novel super-resolution fluorescence lifetime microscopy technique called generalized stepwise optical saturation (GSOS) that generalizes and extends the concept of the recently demonstrated stepwise optical saturation (SOS) super-resolution microscopy [Biomed. Opt. Express9, 1613 (2018)]. The theoretical basis of GSOS is developed based on exploring the dynamics of a two-level fluorophore model and using perturbation theory. We show that although both SOS and GSOS utilize the linear combination of M raw images to increase the imaging resolution by a factor of M , SOS is a special and the simplest case of GSOS. The super-resolution capability is demonstrated with theoretical analysis and numerical simulations for GSOS with sinusoidal and pulse-train modulations. Using GSOS with pulse-train modulation, super-resolution and fluorescence lifetime imaging microscopy (FLIM) images can be obtained simultaneously. The super-resolution FLIM capability is experimentally demonstrated with a cell sample on a custom-built two-photon frequency-domain (FD) FLIM system based on radio frequency analog signal processing. To our knowledge, this is the first implementation of super-resolution imaging in FD-FLIM.
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Affiliation(s)
- Yide Zhang
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
| | - David Benirschke
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
| | - Ola Abdalsalam
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
| | - Scott S. Howard
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
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Zhang Y, Nallathamby PD, Vigil GD, Khan AA, Mason DE, Boerckel JD, Roeder RK, Howard SS. Super-resolution fluorescence microscopy by stepwise optical saturation. BIOMEDICAL OPTICS EXPRESS 2018; 9:1613-1629. [PMID: 29675306 PMCID: PMC5905910 DOI: 10.1364/boe.9.001613] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/02/2018] [Accepted: 03/05/2018] [Indexed: 05/07/2023]
Abstract
Super-resolution fluorescence microscopy is an important tool in biomedical research for its ability to discern features smaller than the diffraction limit. However, due to its difficult implementation and high cost, the super-resolution microscopy is not feasible in many applications. In this paper, we propose and demonstrate a saturation-based super-resolution fluorescence microscopy technique that can be easily implemented and requires neither additional hardware nor complex post-processing. The method is based on the principle of stepwise optical saturation (SOS), where M steps of raw fluorescence images are linearly combined to generate an image with a [Formula: see text]-fold increase in resolution compared with conventional diffraction-limited images. For example, linearly combining (scaling and subtracting) two images obtained at regular powers extends the resolution by a factor of 1.4 beyond the diffraction limit. The resolution improvement in SOS microscopy is theoretically infinite but practically is limited by the signal-to-noise ratio. We perform simulations and experimentally demonstrate super-resolution microscopy with both one-photon (confocal) and multiphoton excitation fluorescence. We show that with the multiphoton modality, the SOS microscopy can provide super-resolution imaging deep in scattering samples.
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Affiliation(s)
- Yide Zhang
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
| | - Prakash D. Nallathamby
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556,
USA
- Notre Dame Center for Nanoscience and Nanotechnology (NDnano), University of Notre Dame, Notre Dame, IN 46556,
USA
| | - Genevieve D. Vigil
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
| | - Aamir A. Khan
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
| | - Devon E. Mason
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
- Departments of Orthopaedic Surgery and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104,
USA
| | - Joel D. Boerckel
- Departments of Orthopaedic Surgery and Bioengineering, University of Pennsylvania, Philadelphia, PA 19104,
USA
| | - Ryan K. Roeder
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556,
USA
- Notre Dame Center for Nanoscience and Nanotechnology (NDnano), University of Notre Dame, Notre Dame, IN 46556,
USA
| | - Scott S. Howard
- Department of Electrical Engineering, University of Notre Dame, Notre Dame, IN 46556,
USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556,
USA
- Notre Dame Center for Nanoscience and Nanotechnology (NDnano), University of Notre Dame, Notre Dame, IN 46556,
USA
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