Boris Hermann | University of Vienna (original) (raw)

Papers by Boris Hermann

Research paper thumbnail of Visible light optical coherence tomography

SPIE Proceedings, 2002

ABSTRACT

Research paper thumbnail of <title>High resolution spectroscopic optical coherence tomography in the 900-1100 nm wavelength range</title>

Coherence Domain Optical Methods in Biomedical Science and Clinical Applications VI, 2002

ABSTRACT

Research paper thumbnail of Sensitivity estimation of spectroscopic optical coherence tomography

SPIE Proceedings, 2002

ABSTRACT

Research paper thumbnail of New wavelength regions for ultrahigh resolution, spectroscopic OCT

Summaries of Papers Presented at the Lasers and Electro-Optics. CLEO '02. Technical Diges

... Speed, High Resolution Capable Optical Delay Line for Imaging Transient Biological Functlon w... more ... Speed, High Resolution Capable Optical Delay Line for Imaging Transient Biological Functlon with Optical Coherence Tomography J. Joshua Reynolds, Daniel L. Marks, and Alex U! Schaefer ... 3. SA Boppart, JG Tearney, BE Bouma, JF Southern, ME Brezinski, and JG Fujimoto. ...

Research paper thumbnail of Precision of quantitative absorption measurement with spectroscopic optical coherence tomography

Optical Coherence Tomography and Coherence Techniques, 2003

ABSTRACT

Research paper thumbnail of Ultrahigh axial resolution optical coherence tomography in the 500-1600 nm region

CLEO, 2003

1. Introduction Optical coherence tomography (OCT) is an imaging technique that measures depth re... more 1. Introduction Optical coherence tomography (OCT) is an imaging technique that measures depth resolved reflectance information of tissue by accommodating a white light interferometer.[1][2][3] Commonly superluminescent diodes are used that typically ...

Research paper thumbnail of Quantification of Photoreceptor Layer Thickness in Normal Eyes Using Optical Coherence Tomography

Retina, 2006

Objective-To demonstrate the ability to segment and analyze individual intraretinal layers, inclu... more Objective-To demonstrate the ability to segment and analyze individual intraretinal layers, including the outer retinal complex (ORC; outer nuclear layer and inner and outer segments of the photoreceptor cells), in healthy eyes using images acquired from the latest commercially available optical coherence tomography (OCT) system (StratusOCT; Carl Zeiss Meditec, Inc., Dublin, CA) and from the ultrahigh resolution OCT (UHR-OCT) prototype. Methods-Thirty-seven eyes from 37 healthy subjects underwent complete ophthalmologic examination using StratusOCT and UHR-OCT. ORC was identified and measured using a segmentation algorithm. Results-For StratusOCT, mean weighted ORC thickness ± SD was 91.1 ± 7.9 µm, and mean weighted total retinal thickness ± SD was determined to be 258.9 ± 10.1 µm. For UHR-OCT, mean weighted ORC thickness ± SD was 96.4 ± 6.3 µm, and mean weighted total retinal thickness ± SD was determined to be 263.4 ± 9.2 µm. There was a higher rate of algorithm failure with UHR-OCT images. Conclusions-Photoreceptor layer thickness can be calculated by measuring ORC on OCT images using a macular segmentation algorithm. ORC values may serve as a useful objective parameter in determining the efficacy of various therapeutic modalities that target the photoreceptor layer in various diseases.

Research paper thumbnail of Using Low Coherent Light for Spectroscopic Information from Tissue

Optical Coherence Tomography, 2008

Research paper thumbnail of Mapping Retinal and Choroidal Thickness in Unilateral Nongranulomatous Acute Anterior Uveitis Using Three-Dimensional 1060-nm Optical Coherence Tomography

Investigative ophthalmology & visual science, Sep 1, 2017

To analyze retinal thickness (RT) and choroidal thickness (ChT) changes in patients with unilater... more To analyze retinal thickness (RT) and choroidal thickness (ChT) changes in patients with unilateral nongranulomatous acute anterior uveitis (AAU) using three-dimensional (3D) 1060-nm optical coherence tomography (OCT). Retinal and choroidal thickness maps were statistically analyzed for 24 patients with newly diagnosed unilateral AAU before therapy. A total of 17 patients were followed until resolution of inflammatory activity (twice in the first week, then weekly). Resolution occurred in all subjects within 6 weeks after the initial diagnosis. After resolution, thickness maps were again generated. All patients were imaged by high-speed spectral-domain (SD) 3D 1060-nm OCT over a 10 × 10-mm field of view. The spatial distribution of retinal and choroidal thickness was mapped and analyzed using the Early Treatment Diabetic Retinopathy Study (ETDRS) grid. The choroid was significantly thicker in eyes affected by AAU than in fellow eyes before therapy with a mean thickness difference of...

Research paper thumbnail of Comparison of UHR-OCT versus Stratus-OCT for definition of early retinal changes after intravitreal Bevacizumab (Avastin®) application in patients with AMD

Spektrum der Augenheilkunde, 2009

To investigate and demonstrate early structural changes of the retina/pigmentepithelial/ chorioca... more To investigate and demonstrate early structural changes of the retina/pigmentepithelial/ choriocapillaris (RPECC) complex before and 10 ± 3 days after intravitreal application of bevacizumab (Avastin ®) in patients with neovascular age related macular degeneration (nAMD) by comparison of standard Stratus Optical Coherence Tomography (S-OCT) and Ultra High Resolution (UHR-OCT) imaging systems. Methods: Six patients with nAMD were examined in a consecutive case series with UHR-OCT and Stratus OCT one day before and 10 ± 3 days after intravitreal application of 1.25 mg (0.125 ml) bevacizumab (Avastin ®). Maximum central retinal thickness (CRT) was measured with the retinal thickness program and calliper measuring function of S-OCT and by the measuring tool of Adobe Photoshop 5.0 in UHR-OCT pictures. Results: In three of six cases residual fluid after treatment was only visible with UHR-OCT but not with the S-OCT. A decrease of maximum CRT could be shown in all cases in UHR-OCT pictures but only in half of the cases (6/3) in S-OCT pictures. In 2/6 cases vitreoretinal adhesions were demonstrable with UHR-OCT but not seen with the S-OCT, irregularities in the photoreceptor layer could be revealed clearly by UHR-OCT in 2/6 cases. Conclusion: After anti-VEGF treatment, UHR-OCT gives more accurate information about residual fluid and intraretinal damage than S-OCT and offers more precise measurements of maximum CRT. These factors may influence further decision of therapy and give us a better explanation and correlation with unsatisfactory visual acuities than with the S-OCT.

Research paper thumbnail of Speckle reduction process based on digital filtering and wavelet compounding in optical coherence tomography for dermatology

Optical Coherence Imaging Techniques and Imaging in Scattering Media, 2015

Optical Coherence Tomography (OCT) has shown a great potential as a complementary imaging tool in... more Optical Coherence Tomography (OCT) has shown a great potential as a complementary imaging tool in the diagnosis of skin diseases. Speckle noise is the most prominent artifact present in OCT images and could limit the interpretation and detection capabilities. In this work we propose a new speckle reduction process and compare it with various denoising filters with high edge-preserving potential, using several sets of dermatological OCT B-scans. To validate the performance we used a custom-designed spectral domain OCT and two different data set groups. The first group consisted in five datasets of a single B-scan captured N times (with N<20), the second were five 3D volumes of 25 Bscans. As quality metrics we used signal to noise (SNR), contrast to noise (CNR) and equivalent number of looks (ENL) ratios. Our results show that a process based on a combination of a 2D enhanced sigma digital filter and a wavelet compounding method achieves the best results in terms of the improvement of the quality metrics. In the first group of individual B-scans we achieved improvements in SNR, CNR and ENL of 16.87 dB, 2.19 and 328 respectively; for the 3D volume datasets the improvements were 15.65 dB, 3.44 and 1148. Our results suggest that the proposed enhancement process may significantly reduce speckle, increasing SNR, CNR and ENL and reducing the number of extra acquisitions of the same frame.

Research paper thumbnail of In vivo Retinal Optical Coherence Tomography at 1030 nm with Enhanced Penetration into the Choroid

Optical Coherence Tomography and Coherence Techniques II, 2005

For the first time in vivo retinal imaging has been performed with a new compact, low noise Yb-ba... more For the first time in vivo retinal imaging has been performed with a new compact, low noise Yb-based ASE source operating in the 1 µm range (NP Photonics, λ c = 1040 nm, ∆ λ = 50 nm, P out = 30 mW) at the dispersion minimum of water with ~7 µm axial resolution. OCT tomograms acquired at 800 nm are compared to those achieved at 1040 nm showing about 200 µm deeper penetration into the choroid below the retinal pigment epithelium. Retinal OCT at longer wavelengths significantly improves the visualization of the retinal pigment epithelium/choriocapillaris/choroid interface and superficial choroidal layers as well as reduces the scattering through turbid media and therefore might provide a better diagnosis tool for early stages of retinal pathologies such as age related macular degeneration which is accompanied by choroidal neovascularization, i.e. extensive growth of new blood vessels in the choroid and retina.

Research paper thumbnail of In vivo three dimensional dual wavelength photoacoustic tomography imaging of the far red fluorescent protein E2-Crimson expressed in adult zebrafish

Biomedical Optics Express, 2013

For the first time the far red fluorescent protein (FP) E2-Crimson genetically expressed in the e... more For the first time the far red fluorescent protein (FP) E2-Crimson genetically expressed in the exocrine pancreas of adult zebrafish has been non-invasively mapped in 3D in vivo using photoacoustic tomography (PAT). The distribution of E2-Crimson in the exocrine pancreas acquired by PAT was confirmed using epifluorescence imaging and histology, with optical coherence tomography (OCT) providing complementary structural information. This work demonstrates the depth advantage of PAT to resolve FP in an animal model and establishes the value of E2-Crimson for PAT studies of transgenic models, laying the foundation for future longitudinal studies of the zebrafish as a model of diseases affecting inner organs.

Research paper thumbnail of An Achromatized Endoscope for Ultrahigh-Resolution Optical Coherence Tomography

Optical Coherence Tomography and Coherence Techniques II, 2005

Mouse models are increasingly important for studying human GI pathology. OCT provides minimally i... more Mouse models are increasingly important for studying human GI pathology. OCT provides minimally invasive, cross-sectional images that indicate the thickness and scattering density of underlying tissue. We have developed endoscopic ultrahigh resolution OCT (UHR-OCT) to imaging mouse colon in vivo. The reduced scale of the mouse colon makes tissue light penetration much less problematic, and high resolution acutely necessary. Higher lateral resolution requires a departure from the traditional cemented GRIN lens design. We support the need for better chromatic aberration than can be achieved by a GRIN lens using commercial raytracing software. We have designed and built a 2mm diameter endoscopic UHR-OCT system achromatized for 770-1020nm for use with a Titanium:sapphire laser with 260 nm bandwidth at full-width-half-maximum centered at 800 nm while achieving a 4.4um lateral spot dimension at focus. A pair of KZFSN5/SFPL53 doublets provides excellent primary and secondary color correction to maintain wide bandwidth through the imaging depth. A slight deviation from normal beam exit angle suppresses collection of the strong back reflection at the exit window surface. The novel design endoscope was built and characterized for through focus bandwidth, axial resolution, signal to noise, and lateral spot dimension. Performance is demonstrated on in vivo mouse colon. Ultrahigh-resolution images of mouse tissue enable the visualization of microscopic features, including crypts that have previously been observed with standard resolution OCT in humans but were too small to see in mouse tissue. Resolution near the cellular level is potentially capable of identifying abnormal crypt formation and dysplastic cellular organization.

Research paper thumbnail of Optophysiology: Depth-resolved probing of retinal physiology with functional ultrahigh-resolution optical coherence tomography

Proceedings of the National Academy of Sciences, 2006

Noncontact, depth-resolved, optical probing of retinal response to visual stimulation with a <... more Noncontact, depth-resolved, optical probing of retinal response to visual stimulation with a <10-μm spatial resolution, achieved by using functional ultrahigh-resolution optical coherence tomography (fUHROCT), is demonstrated in isolated rabbit retinas. The method takes advantage of the fact that physiological changes in dark-adapted retinas caused by light stimulation can result in local variation of the tissue reflectivity. fUHROCT scans were acquired from isolated retinas synchronously with electrical recordings before, during, and after light stimulation. Pronounced stimulus-related changes in the retinal reflectivity profile were observed in the inner/outer segments of the photoreceptor layer and the plexiform layers. Control experiments (e.g., dark adaptation vs. light stimulation), pharmacological inhibition of photoreceptor function, and synaptic transmission to the inner retina confirmed that the origin of the observed optical changes is the altered physiological state o...

Research paper thumbnail of Ultrahigh resolution Fourier domain optical coherence tomography

Optics Express, 2004

In the last 10 years, Optical Coherence Tomography (OCT) has been successfully applied to art con... more In the last 10 years, Optical Coherence Tomography (OCT) has been successfully applied to art conservation, history and archaeology. OCT has the potential to become a routine non-invasive tool in museums allowing cross-section imaging anywhere on an intact object where there are no other methods of obtaining subsurface information. While current commercial OCTs have shown potential in this field, they are still limited in depth resolution (> 4 μm in paint and varnish) compared to conventional microscopic examination of sampled paint cross-sections (~1 μm). An ultrahigh resolution fiber-based Fourier domain optical coherence tomography system with a constant axial resolution of 1.2 μm in varnish or paint throughout a depth range of 1.5 mm has been developed. While Fourier domain OCT of similar resolution has been demonstrated recently, the sensitivity roll-off of some of these systems are still significant. In contrast, this current system achieved a sensitivity roll-off that is less than 2 dB over a 1.2 mm depth range with an incident power of ~1 mW on the sample. The high resolution and sensitivity of the system makes it convenient to image thin varnish and glaze layers with unprecedented contrast. The non-invasive 'virtual' cross-section images obtained with the system show the thin varnish layers with similar resolution in the depth direction but superior clarity in the layer interfaces when compared with conventional optical microscope images of actual paint sample cross-sections obtained microdestructively.

Research paper thumbnail of Full-field time-encoded frequency-domain optical coherence tomography

Research paper thumbnail of Fast dispersion encoded full range optical coherence tomography for retinal imaging at 800 nm and 1060 nm

Optics Express, 2010

The dispersion mismatch between sample and reference arm in frequency-domain optical coherence to... more The dispersion mismatch between sample and reference arm in frequency-domain optical coherence tomography (OCT) can be used to iteratively suppress complex conjugate artifacts and thereby increase the imaging range. In this paper, we propose a fast dispersion encoded full range (DEFR) algorithm that detects multiple signal components per iteration. The influence of different dispersion levels on the reconstruction quality is analyzed experimentally using a multilayered scattering phantom and in vivo retinal tomograms at 800 nm. Best results have been achieved with 30 mm SF11, with neglectable resolution decrease due to finite resolution of the spectrometer. Our fast DEFR algorithm achieves an average suppression ratio of 55 dB and typically converges within 5 to 10 iterations. The processing time on non-dedicated hardware was 5 to 10 seconds for tomograms with 512 depth scans and 4096 sampling points per depth scan. Application of DEFR to the more challenging 1060 nm wavelength region is also demonstrated by introducing an additional optical fibre in the sample arm.

Research paper thumbnail of Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis

Optics Express, 2010

A novel statistical model based on texture and shape for fully automatic intraretinal layer segme... more A novel statistical model based on texture and shape for fully automatic intraretinal layer segmentation of normal retinal tomograms obtained by a commercial 800nm optical coherence tomography (OCT) system is developed. While existing algorithms often fail dramatically due to strong speckle noise, non-optimal imaging conditions, shadows and other artefacts, the novel algorithm's accuracy only slowly deteriorates when progressively increasing segmentation task difficulty. Evaluation against a large set of manual segmentations shows unprecedented robustness, even in the presence of additional strong speckle noise, with dynamic range tested down to 12dB, enabling segmentation of almost all intraretinal layers in cases previously inaccessible to the existing algorithms. For the first time, an error measure is computed from a large, representative manually segmented data set (466 B-scans from 17 eyes, segmented twice by different operators) and compared to the automatic segmentation with a difference of only 2.6% against the inter-observer variability.

Research paper thumbnail of Wide-Field Optical Coherence Tomography of the Choroid In Vivo

Investigative Ophthalmology & Visual Science, 2008

PURPOSE. To demonstrate high-speed, high axial resolution optical coherence tomography (OCT) at 1... more PURPOSE. To demonstrate high-speed, high axial resolution optical coherence tomography (OCT) at 1060 nm with penetration to the sclera. The clinical feasibility of dense, high-speed sampling for higher levels of detail at the macula and optic nerve head is explored with respect to motion artifacts. METHODS. A three-dimensional (3D) OCT system making use of a high-speed camera operating at 47,000 depth scans/s was developed. The 1010-to 1080-nm wavelength band leads to 6.7 m effective axial resolution and enables the acquisition of retinal and choroidal 130 Megavoxel volumes of human subjects within 7 seconds. Motion artifacts were reduced by numeric postprocessing techniques. RESULTS. Drift motion artifacts could be suppressed within fields up to 38°ϫ 38°(approximately 1 cm 2) using acquisition speeds of up to 74 frames/s at 512 ϫ 512 pixel/frame. This isotropic OCT sampling of the human retina in vivo allowed reconstruction of the retinal microvasculature solely on vessel reflectivity, without the use of contrast agents, and revealed three interconnected capillary meshworks. Simultaneously in the choroid, the structure of the choriocapillaris, Sattler's layer, and Haller's layer were differentiated, and the choroidal-scleral interface was clearly delineated in densely sampled narrowand wide-angle scans (Ͼ38°). At the optic nerve head, the 3D fine structure of the lamina cribrosa and the circle of Zinn-Haller were visualized. CONCLUSIONS. OCT almost centered within the 1060-nm water transmission window significantly profits from lower scattering and allows investigation of the retina and choroid at an unprecedented combination of penetration and high speed at high resolution and may provide superior clinical feasibility to commercial 800-nm devices.

Research paper thumbnail of Visible light optical coherence tomography

SPIE Proceedings, 2002

ABSTRACT

Research paper thumbnail of <title>High resolution spectroscopic optical coherence tomography in the 900-1100 nm wavelength range</title>

Coherence Domain Optical Methods in Biomedical Science and Clinical Applications VI, 2002

ABSTRACT

Research paper thumbnail of Sensitivity estimation of spectroscopic optical coherence tomography

SPIE Proceedings, 2002

ABSTRACT

Research paper thumbnail of New wavelength regions for ultrahigh resolution, spectroscopic OCT

Summaries of Papers Presented at the Lasers and Electro-Optics. CLEO '02. Technical Diges

... Speed, High Resolution Capable Optical Delay Line for Imaging Transient Biological Functlon w... more ... Speed, High Resolution Capable Optical Delay Line for Imaging Transient Biological Functlon with Optical Coherence Tomography J. Joshua Reynolds, Daniel L. Marks, and Alex U! Schaefer ... 3. SA Boppart, JG Tearney, BE Bouma, JF Southern, ME Brezinski, and JG Fujimoto. ...

Research paper thumbnail of Precision of quantitative absorption measurement with spectroscopic optical coherence tomography

Optical Coherence Tomography and Coherence Techniques, 2003

ABSTRACT

Research paper thumbnail of Ultrahigh axial resolution optical coherence tomography in the 500-1600 nm region

CLEO, 2003

1. Introduction Optical coherence tomography (OCT) is an imaging technique that measures depth re... more 1. Introduction Optical coherence tomography (OCT) is an imaging technique that measures depth resolved reflectance information of tissue by accommodating a white light interferometer.[1][2][3] Commonly superluminescent diodes are used that typically ...

Research paper thumbnail of Quantification of Photoreceptor Layer Thickness in Normal Eyes Using Optical Coherence Tomography

Retina, 2006

Objective-To demonstrate the ability to segment and analyze individual intraretinal layers, inclu... more Objective-To demonstrate the ability to segment and analyze individual intraretinal layers, including the outer retinal complex (ORC; outer nuclear layer and inner and outer segments of the photoreceptor cells), in healthy eyes using images acquired from the latest commercially available optical coherence tomography (OCT) system (StratusOCT; Carl Zeiss Meditec, Inc., Dublin, CA) and from the ultrahigh resolution OCT (UHR-OCT) prototype. Methods-Thirty-seven eyes from 37 healthy subjects underwent complete ophthalmologic examination using StratusOCT and UHR-OCT. ORC was identified and measured using a segmentation algorithm. Results-For StratusOCT, mean weighted ORC thickness ± SD was 91.1 ± 7.9 µm, and mean weighted total retinal thickness ± SD was determined to be 258.9 ± 10.1 µm. For UHR-OCT, mean weighted ORC thickness ± SD was 96.4 ± 6.3 µm, and mean weighted total retinal thickness ± SD was determined to be 263.4 ± 9.2 µm. There was a higher rate of algorithm failure with UHR-OCT images. Conclusions-Photoreceptor layer thickness can be calculated by measuring ORC on OCT images using a macular segmentation algorithm. ORC values may serve as a useful objective parameter in determining the efficacy of various therapeutic modalities that target the photoreceptor layer in various diseases.

Research paper thumbnail of Using Low Coherent Light for Spectroscopic Information from Tissue

Optical Coherence Tomography, 2008

Research paper thumbnail of Mapping Retinal and Choroidal Thickness in Unilateral Nongranulomatous Acute Anterior Uveitis Using Three-Dimensional 1060-nm Optical Coherence Tomography

Investigative ophthalmology & visual science, Sep 1, 2017

To analyze retinal thickness (RT) and choroidal thickness (ChT) changes in patients with unilater... more To analyze retinal thickness (RT) and choroidal thickness (ChT) changes in patients with unilateral nongranulomatous acute anterior uveitis (AAU) using three-dimensional (3D) 1060-nm optical coherence tomography (OCT). Retinal and choroidal thickness maps were statistically analyzed for 24 patients with newly diagnosed unilateral AAU before therapy. A total of 17 patients were followed until resolution of inflammatory activity (twice in the first week, then weekly). Resolution occurred in all subjects within 6 weeks after the initial diagnosis. After resolution, thickness maps were again generated. All patients were imaged by high-speed spectral-domain (SD) 3D 1060-nm OCT over a 10 × 10-mm field of view. The spatial distribution of retinal and choroidal thickness was mapped and analyzed using the Early Treatment Diabetic Retinopathy Study (ETDRS) grid. The choroid was significantly thicker in eyes affected by AAU than in fellow eyes before therapy with a mean thickness difference of...

Research paper thumbnail of Comparison of UHR-OCT versus Stratus-OCT for definition of early retinal changes after intravitreal Bevacizumab (Avastin®) application in patients with AMD

Spektrum der Augenheilkunde, 2009

To investigate and demonstrate early structural changes of the retina/pigmentepithelial/ chorioca... more To investigate and demonstrate early structural changes of the retina/pigmentepithelial/ choriocapillaris (RPECC) complex before and 10 ± 3 days after intravitreal application of bevacizumab (Avastin ®) in patients with neovascular age related macular degeneration (nAMD) by comparison of standard Stratus Optical Coherence Tomography (S-OCT) and Ultra High Resolution (UHR-OCT) imaging systems. Methods: Six patients with nAMD were examined in a consecutive case series with UHR-OCT and Stratus OCT one day before and 10 ± 3 days after intravitreal application of 1.25 mg (0.125 ml) bevacizumab (Avastin ®). Maximum central retinal thickness (CRT) was measured with the retinal thickness program and calliper measuring function of S-OCT and by the measuring tool of Adobe Photoshop 5.0 in UHR-OCT pictures. Results: In three of six cases residual fluid after treatment was only visible with UHR-OCT but not with the S-OCT. A decrease of maximum CRT could be shown in all cases in UHR-OCT pictures but only in half of the cases (6/3) in S-OCT pictures. In 2/6 cases vitreoretinal adhesions were demonstrable with UHR-OCT but not seen with the S-OCT, irregularities in the photoreceptor layer could be revealed clearly by UHR-OCT in 2/6 cases. Conclusion: After anti-VEGF treatment, UHR-OCT gives more accurate information about residual fluid and intraretinal damage than S-OCT and offers more precise measurements of maximum CRT. These factors may influence further decision of therapy and give us a better explanation and correlation with unsatisfactory visual acuities than with the S-OCT.

Research paper thumbnail of Speckle reduction process based on digital filtering and wavelet compounding in optical coherence tomography for dermatology

Optical Coherence Imaging Techniques and Imaging in Scattering Media, 2015

Optical Coherence Tomography (OCT) has shown a great potential as a complementary imaging tool in... more Optical Coherence Tomography (OCT) has shown a great potential as a complementary imaging tool in the diagnosis of skin diseases. Speckle noise is the most prominent artifact present in OCT images and could limit the interpretation and detection capabilities. In this work we propose a new speckle reduction process and compare it with various denoising filters with high edge-preserving potential, using several sets of dermatological OCT B-scans. To validate the performance we used a custom-designed spectral domain OCT and two different data set groups. The first group consisted in five datasets of a single B-scan captured N times (with N<20), the second were five 3D volumes of 25 Bscans. As quality metrics we used signal to noise (SNR), contrast to noise (CNR) and equivalent number of looks (ENL) ratios. Our results show that a process based on a combination of a 2D enhanced sigma digital filter and a wavelet compounding method achieves the best results in terms of the improvement of the quality metrics. In the first group of individual B-scans we achieved improvements in SNR, CNR and ENL of 16.87 dB, 2.19 and 328 respectively; for the 3D volume datasets the improvements were 15.65 dB, 3.44 and 1148. Our results suggest that the proposed enhancement process may significantly reduce speckle, increasing SNR, CNR and ENL and reducing the number of extra acquisitions of the same frame.

Research paper thumbnail of In vivo Retinal Optical Coherence Tomography at 1030 nm with Enhanced Penetration into the Choroid

Optical Coherence Tomography and Coherence Techniques II, 2005

For the first time in vivo retinal imaging has been performed with a new compact, low noise Yb-ba... more For the first time in vivo retinal imaging has been performed with a new compact, low noise Yb-based ASE source operating in the 1 µm range (NP Photonics, λ c = 1040 nm, ∆ λ = 50 nm, P out = 30 mW) at the dispersion minimum of water with ~7 µm axial resolution. OCT tomograms acquired at 800 nm are compared to those achieved at 1040 nm showing about 200 µm deeper penetration into the choroid below the retinal pigment epithelium. Retinal OCT at longer wavelengths significantly improves the visualization of the retinal pigment epithelium/choriocapillaris/choroid interface and superficial choroidal layers as well as reduces the scattering through turbid media and therefore might provide a better diagnosis tool for early stages of retinal pathologies such as age related macular degeneration which is accompanied by choroidal neovascularization, i.e. extensive growth of new blood vessels in the choroid and retina.

Research paper thumbnail of In vivo three dimensional dual wavelength photoacoustic tomography imaging of the far red fluorescent protein E2-Crimson expressed in adult zebrafish

Biomedical Optics Express, 2013

For the first time the far red fluorescent protein (FP) E2-Crimson genetically expressed in the e... more For the first time the far red fluorescent protein (FP) E2-Crimson genetically expressed in the exocrine pancreas of adult zebrafish has been non-invasively mapped in 3D in vivo using photoacoustic tomography (PAT). The distribution of E2-Crimson in the exocrine pancreas acquired by PAT was confirmed using epifluorescence imaging and histology, with optical coherence tomography (OCT) providing complementary structural information. This work demonstrates the depth advantage of PAT to resolve FP in an animal model and establishes the value of E2-Crimson for PAT studies of transgenic models, laying the foundation for future longitudinal studies of the zebrafish as a model of diseases affecting inner organs.

Research paper thumbnail of An Achromatized Endoscope for Ultrahigh-Resolution Optical Coherence Tomography

Optical Coherence Tomography and Coherence Techniques II, 2005

Mouse models are increasingly important for studying human GI pathology. OCT provides minimally i... more Mouse models are increasingly important for studying human GI pathology. OCT provides minimally invasive, cross-sectional images that indicate the thickness and scattering density of underlying tissue. We have developed endoscopic ultrahigh resolution OCT (UHR-OCT) to imaging mouse colon in vivo. The reduced scale of the mouse colon makes tissue light penetration much less problematic, and high resolution acutely necessary. Higher lateral resolution requires a departure from the traditional cemented GRIN lens design. We support the need for better chromatic aberration than can be achieved by a GRIN lens using commercial raytracing software. We have designed and built a 2mm diameter endoscopic UHR-OCT system achromatized for 770-1020nm for use with a Titanium:sapphire laser with 260 nm bandwidth at full-width-half-maximum centered at 800 nm while achieving a 4.4um lateral spot dimension at focus. A pair of KZFSN5/SFPL53 doublets provides excellent primary and secondary color correction to maintain wide bandwidth through the imaging depth. A slight deviation from normal beam exit angle suppresses collection of the strong back reflection at the exit window surface. The novel design endoscope was built and characterized for through focus bandwidth, axial resolution, signal to noise, and lateral spot dimension. Performance is demonstrated on in vivo mouse colon. Ultrahigh-resolution images of mouse tissue enable the visualization of microscopic features, including crypts that have previously been observed with standard resolution OCT in humans but were too small to see in mouse tissue. Resolution near the cellular level is potentially capable of identifying abnormal crypt formation and dysplastic cellular organization.

Research paper thumbnail of Optophysiology: Depth-resolved probing of retinal physiology with functional ultrahigh-resolution optical coherence tomography

Proceedings of the National Academy of Sciences, 2006

Noncontact, depth-resolved, optical probing of retinal response to visual stimulation with a <... more Noncontact, depth-resolved, optical probing of retinal response to visual stimulation with a <10-μm spatial resolution, achieved by using functional ultrahigh-resolution optical coherence tomography (fUHROCT), is demonstrated in isolated rabbit retinas. The method takes advantage of the fact that physiological changes in dark-adapted retinas caused by light stimulation can result in local variation of the tissue reflectivity. fUHROCT scans were acquired from isolated retinas synchronously with electrical recordings before, during, and after light stimulation. Pronounced stimulus-related changes in the retinal reflectivity profile were observed in the inner/outer segments of the photoreceptor layer and the plexiform layers. Control experiments (e.g., dark adaptation vs. light stimulation), pharmacological inhibition of photoreceptor function, and synaptic transmission to the inner retina confirmed that the origin of the observed optical changes is the altered physiological state o...

Research paper thumbnail of Ultrahigh resolution Fourier domain optical coherence tomography

Optics Express, 2004

In the last 10 years, Optical Coherence Tomography (OCT) has been successfully applied to art con... more In the last 10 years, Optical Coherence Tomography (OCT) has been successfully applied to art conservation, history and archaeology. OCT has the potential to become a routine non-invasive tool in museums allowing cross-section imaging anywhere on an intact object where there are no other methods of obtaining subsurface information. While current commercial OCTs have shown potential in this field, they are still limited in depth resolution (> 4 μm in paint and varnish) compared to conventional microscopic examination of sampled paint cross-sections (~1 μm). An ultrahigh resolution fiber-based Fourier domain optical coherence tomography system with a constant axial resolution of 1.2 μm in varnish or paint throughout a depth range of 1.5 mm has been developed. While Fourier domain OCT of similar resolution has been demonstrated recently, the sensitivity roll-off of some of these systems are still significant. In contrast, this current system achieved a sensitivity roll-off that is less than 2 dB over a 1.2 mm depth range with an incident power of ~1 mW on the sample. The high resolution and sensitivity of the system makes it convenient to image thin varnish and glaze layers with unprecedented contrast. The non-invasive 'virtual' cross-section images obtained with the system show the thin varnish layers with similar resolution in the depth direction but superior clarity in the layer interfaces when compared with conventional optical microscope images of actual paint sample cross-sections obtained microdestructively.

Research paper thumbnail of Full-field time-encoded frequency-domain optical coherence tomography

Research paper thumbnail of Fast dispersion encoded full range optical coherence tomography for retinal imaging at 800 nm and 1060 nm

Optics Express, 2010

The dispersion mismatch between sample and reference arm in frequency-domain optical coherence to... more The dispersion mismatch between sample and reference arm in frequency-domain optical coherence tomography (OCT) can be used to iteratively suppress complex conjugate artifacts and thereby increase the imaging range. In this paper, we propose a fast dispersion encoded full range (DEFR) algorithm that detects multiple signal components per iteration. The influence of different dispersion levels on the reconstruction quality is analyzed experimentally using a multilayered scattering phantom and in vivo retinal tomograms at 800 nm. Best results have been achieved with 30 mm SF11, with neglectable resolution decrease due to finite resolution of the spectrometer. Our fast DEFR algorithm achieves an average suppression ratio of 55 dB and typically converges within 5 to 10 iterations. The processing time on non-dedicated hardware was 5 to 10 seconds for tomograms with 512 depth scans and 4096 sampling points per depth scan. Application of DEFR to the more challenging 1060 nm wavelength region is also demonstrated by introducing an additional optical fibre in the sample arm.

Research paper thumbnail of Robust segmentation of intraretinal layers in the normal human fovea using a novel statistical model based on texture and shape analysis

Optics Express, 2010

A novel statistical model based on texture and shape for fully automatic intraretinal layer segme... more A novel statistical model based on texture and shape for fully automatic intraretinal layer segmentation of normal retinal tomograms obtained by a commercial 800nm optical coherence tomography (OCT) system is developed. While existing algorithms often fail dramatically due to strong speckle noise, non-optimal imaging conditions, shadows and other artefacts, the novel algorithm's accuracy only slowly deteriorates when progressively increasing segmentation task difficulty. Evaluation against a large set of manual segmentations shows unprecedented robustness, even in the presence of additional strong speckle noise, with dynamic range tested down to 12dB, enabling segmentation of almost all intraretinal layers in cases previously inaccessible to the existing algorithms. For the first time, an error measure is computed from a large, representative manually segmented data set (466 B-scans from 17 eyes, segmented twice by different operators) and compared to the automatic segmentation with a difference of only 2.6% against the inter-observer variability.

Research paper thumbnail of Wide-Field Optical Coherence Tomography of the Choroid In Vivo

Investigative Ophthalmology & Visual Science, 2008

PURPOSE. To demonstrate high-speed, high axial resolution optical coherence tomography (OCT) at 1... more PURPOSE. To demonstrate high-speed, high axial resolution optical coherence tomography (OCT) at 1060 nm with penetration to the sclera. The clinical feasibility of dense, high-speed sampling for higher levels of detail at the macula and optic nerve head is explored with respect to motion artifacts. METHODS. A three-dimensional (3D) OCT system making use of a high-speed camera operating at 47,000 depth scans/s was developed. The 1010-to 1080-nm wavelength band leads to 6.7 m effective axial resolution and enables the acquisition of retinal and choroidal 130 Megavoxel volumes of human subjects within 7 seconds. Motion artifacts were reduced by numeric postprocessing techniques. RESULTS. Drift motion artifacts could be suppressed within fields up to 38°ϫ 38°(approximately 1 cm 2) using acquisition speeds of up to 74 frames/s at 512 ϫ 512 pixel/frame. This isotropic OCT sampling of the human retina in vivo allowed reconstruction of the retinal microvasculature solely on vessel reflectivity, without the use of contrast agents, and revealed three interconnected capillary meshworks. Simultaneously in the choroid, the structure of the choriocapillaris, Sattler's layer, and Haller's layer were differentiated, and the choroidal-scleral interface was clearly delineated in densely sampled narrowand wide-angle scans (Ͼ38°). At the optic nerve head, the 3D fine structure of the lamina cribrosa and the circle of Zinn-Haller were visualized. CONCLUSIONS. OCT almost centered within the 1060-nm water transmission window significantly profits from lower scattering and allows investigation of the retina and choroid at an unprecedented combination of penetration and high speed at high resolution and may provide superior clinical feasibility to commercial 800-nm devices.