R-3 Repository :: Browsing by Author "Tkaczyk, Tomasz S."

Browsing by Author "Tkaczyk, Tomasz S."

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3D printed fiber optic faceplates by custom controlled fused deposition modeling
(Optical Society of America, 2018) Wang, Ye; Gawedzinski, John; Pawlowski, Michal E.; Tkaczyk, Tomasz S.
A 3D printing technique for manufacturing air-clad coherent fiber optic faceplates is presented. The custom G-code programming is implemented on a fused deposition modeling (FDM) desktop printer to additively draw optical fibers using high-transparency thermoplastic filaments. The 3D printed faceplate consists of 20000 fibers and achieves spatial resolution 1.78 LP/mm. Transmission loss and crosstalk are characterized and compared among the faceplates printed from four kinds of transparent filaments as well as different faceplate thicknesses. The printing temperature is verified by testing the transmission of the faceplates printed under different temperatures. Compared with the conventional stack-and-draw fabrication, the FDM 3D printing technique simplifies the fabrication procedure. The ability to draw fibers with arbitrary organization, structure and overall shape provides additional degree of freedom to opto-mechanical design. Our results indicate a promising capability of 3D printing as the manufacturing technology for fiber optical devices.
A Dye-Free Analog to Retinal Angiography Using Hyperspectral Unmixing to Retrieve Oxyhemoglobin Abundance
(ARVO, 2019) Dwight, Jason G.; Weng, Christina Y.; Pawlowski, Michal E.; Tkaczyk, Tomasz S.
Purpose: Retinal angiography evaluates retinal and choroidal perfusion and vascular integrity and is used to manage many ophthalmic diseases, such as age-related macular degeneration. The most common method, fluorescein angiography (FA), is invasive and can lead to untoward effects. As an emerging replacement, noninvasive OCT angiography (OCTA) is used regularly as a dye-free substitute with superior resolution and additional depth-sectioning abilities; however, general trends in FA as signified by varying intensity in images are not always reproducible in the fine structural detail in an OCTA image stack because of the source of their respective signals, OCT speckle decorrelation versus fluorescein emission. Methods: We present a noninvasive/dye-free analog to angiography imaging using retinal hyperspectral imaging with a nonscanning spectral imager, the image mapping spectrometer (IMS), to reproduce perfusion-related data based on the abundance of oxyhemoglobin (HbO2) in the retina. With a new unmixing procedure of the IMS-acquired spectral data cubes (350 × 350 × 43), we produced noninvasive HbO2 maps unmixed from reflectance spectra. Results: Here, we present 15 HbO2 maps from seven healthy and eight diseased retinas and compare these maps with corresponding FA and OCTA results with a discussion of each technique. Conclusions: Our maps showed visual agreement with hypo- and hyperfluorescence trends in venous phase FA images, suggesting that our method provides a new use for hyperspectral imaging as a noninvasive angiography-analog technique and as a complementary technique to OCTA. Translational Relevance: The application of hyperspectral imaging and spectral analysis can potentially improve/broaden retinal disease screening and enable a noninvasive technique, which complements OCTA.
A real-time snapshot hyperspectral endoscope and miniature endomicroscopy objectives for a two field-of-view (Bi-FOV) endoscope
(2010) Kester, Robert Timothy; Tkaczyk, Tomasz S.
This thesis focuses on the development of two novel imaging technologies which will serve as the basis for the future development of a two field-of-view or "Bi-FOV" endoscope capable of imaging at both microscopic and macroscopic regimes simultaneously. The goal of the Bi-FOV is to provide clinicians with a better tool for pre- and early cancer detection. The first technology developed makes it possible to obtain low cost, high performance, miniature optical systems for use in the microscopic portion of the Bi-FOV endoscope. The second technology developed for the Bi-FOV is a real-time snapshot hyperspectral endoscope called the IMS endoscope. The IMS endoscope is based on an image mapping technique which is capable of achieving high temporal and spatial resolution, excellent optical throughput, and low costs. The parallel, high throughput nature of this technique enables the device to operate at frame rates of 5.2 fps while collecting a 3D (x, y, gamma ) datacube of 350 x 350 x 48. We have successfully imaged tissue in vivo resolving tissue vasculature and oxy-hemoglobin which are important early cancer biomarkers.
Achromatized endomicroscope objective for optical biopsy
(Optical Society of America, 2013) Kyrish, Matthew; Tkaczyk, Tomasz S.
Currently, researchers and clinicians lack achromatized endomicroscope objectives that are as narrow as biopsy needles. We present a proof-of-concept prototype that validates the optical design of an NA0.4 objective. The objective, built with plastic lenses, has a 0.9 mm clear aperture and is achromatized from 452 nm to 623 nm. The objective’s measured Strehl ratio is 0.74 ± 0.05 across a 250 μm FOV. We perform optical sectioning via structured illumination through the objective while capturing fluorescence images of breast carcinoma cells stained with proflavine and cresyl violet. This technology has the potential to improve optical biopsies and provide the next step forward in cancer diagnostics.
Additive manufacturing for the development of optical/photonic systems and components
(Optica Publishing Group, 2022) Berglund, Gregory; Wisniowiecki, Anna; Gawedzinski, John; Applegate, Brian; Tkaczyk, Tomasz S.
The ambition of this review is to provide an up-to-date synopsis of the state of 3D printing technology for optical and photonic components, to gauge technological advances, and to discuss future opportunities. While a range of approaches have been developed and some have been commercialized, no single approach can yet simultaneously achieve small detail and low roughness at large print volumes and speed using multiple materials. Instead, each approach occupies a niche where the components/structures that can be created fit within a relatively narrow range of geometries with limited material choices. For instance, the common Fused Deposition Modeling (FDM) approach is capable of large print volumes at relatively high speeds but lacks the resolution needed for small detail (>100µm) with low roughness (>9µm). At the other end of the spectrum, two-photon polymerization can achieve roughness (<15nm) and detail (<140nm) comparable to commercial molded and polished optics. However, the practical achievable print volume and speed are orders of magnitude smaller and slower than the FDM approach. Herein, we discuss the current state-of-the-art 3D printing approaches, noting the capability of each approach and prognosticate on future innovations that could close the gaps in performance.
All-plastic, miniature, digital fluorescence microscope for three part white blood cell differential measurements at the point of care
(The Optical Society, 2015) Forcucci, Alessandra; Pawlowski, Michal E.; Majors, Catherine; Richards-Kortum, Rebecca; Tkaczyk, Tomasz S.
Three-part differential white blood cell counts are used for disease diagnosis and monitoring at the point-of-care. A low-cost, miniature achromatic microscope was fabricated for identification of lymphocytes, monocytes, and granulocytes in samples of whole blood stained with acridine orange. The microscope was manufactured using rapid prototyping techniques of diamond turning and 3D printing and is intended for use at the point-of-care in low-resource settings. The custom-designed microscope requires no manual adjustment between samples and was successfully able to classify three white blood cell types (lymphocytes, granulocytes, and monocytes) using samples of peripheral whole blood stained with acridine orange.
Array microscopy technology and its application to digital detection of Mycobacterium tuberculosis
(2013-09-16) McCall, Brian; Tkaczyk, Tomasz S.; Richards-Kortum, Rebecca Rae; Graviss, Edward A.; Baraniuk, Richard G.
Tuberculosis causes more deaths worldwide than any other curable infectious disease. This is the case despite tuberculosis appearing to be on the verge of eradication midway through the last century. Efforts at reversing the spread of tuberculosis have intensified since the early 1990s. Since then, microscopy has been the primary frontline diagnostic. In this dissertation, advances in clinical microscopy towards array microscopy for digital detection of Mycobacterium tuberculosis are presented. Digital array microscopy separates the tasks of microscope operation and pathogen detection and will reduce the specialization needed in order to operate the microscope. Distributing the work and reducing specialization will allow this technology to be deployed at the point of care, taking the front-line diagnostic for tuberculosis from the microscopy center to the community health center. By improving access to microscopy centers, hundreds of thousands of lives can be saved. For this dissertation, a lens was designed that can be manufactured as 4×6 array of microscopes. This lens design is diffraction limited, having less than 0.071 waves of aberration (root mean square) over the entire field of view. A total area imaged onto a full-frame digital image sensor is expected to be 3.94 mm2, which according to tuberculosis microscopy guidelines is more than sufficient for a sensitive diagnosis. The design is tolerant to single point diamond turning manufacturing errors, as found by tolerance analysis and by fabricating a prototype. Diamond micro-milling, a fabrication technique for lens array molds, was applied to plastic plano-concave and plano-convex lens arrays, and found to produce high quality optical surfaces. The micro-milling technique did not prove robust enough to produce bi-convex and meniscus lens arrays in a variety of lens shapes, however, and it required lengthy fabrication times. In order to rapidly prototype new lenses, a new diamond machining technique was developed called 4-axis single point diamond machining. This technique is 2-10x faster than micro-milling, depending on how advanced the micro-milling equipment is. With array microscope fabrication still in development, a single prototype of the lens designed for an array microscope was fabricated using single point diamond turning. The prototype microscope objective was validated in a pre-clinical trial. The prototype was compared with a standard clinical microscope objective in diagnostic tests. High concordance, a Fleiss’s kappa of 0.88, was found between diagnoses made using the prototype and standard microscope objectives and a reference test. With the lens designed and validated and an advanced fabrication process developed, array microscopy technology is advanced to the point where it is feasible to rapidly prototype an array microscope for detection of tuberculosis and translate array microscope from an innovative concept to a device that can save lives.
Clinical training and validation of the LeukoScope: a low-cost, point-of-care device to perform white blood cell and neutrophil counts
(Royal Society of Chemistry, 2019) Majors, Catherine E.; Pawlowski, Michal E.; Burke, Daniel C.; Tkaczyk, Tomasz S.; Rieber, Alyssa; Richards-Kortum, Rebecca
A white blood cell (WBC) count with partial differential is an important clinical laboratory test. However, current methods to perform a WBC count and differential are difficult to use at the point of care or too expensive for use in low-resource settings. To meet this need, we developed the LeukoScope: a low-cost system to measure a WBC and neutrophil count from a single drop of blood at the point of care. The LeukoScope is battery powered and has a sample-to-answer time of <5 minutes. A drop of blood from a finger stick is added to a LeukoScope sample cartridge where pre-dried acridine orange fluorescently stains WBCs. The cartridge is then inserted into the LeukoScope reader where a portable fluorescence microscope captures a color image of the sample, which is analyzed to report results to the user. The LeukoScope system was tested at the point of care using fingerprick samples collected from 105 general oncology patients in Houston, TX. Performance of the LeukoScope was compared to that of a HemoCue WBC DIFF performed using the same fingerprick sample; clinical laboratory analysis of a venous blood draw was used as the gold standard in all cases. Bland–Altman analysis showed that the LeukoScope and HemoCue WBC DIFF had similar accuracy for measurement of WBC and neutrophil counts as compared to the gold standard. Seven out of eight patients with abnormal WBC count values were correctly identified using the LeukoScope, while six out of eight were correctly identified using the HemoCue WBC DIFF. Five out of six patients with abnormal neutrophil counts were correctly identified using the LeukoScope, while six of six were correctly identified using the HemoCue WBC DIFF.
Development of a multimodal foveated endomicroscope for the detection of oral cancer
(The Optical Society, 2017) Shadfan, Adam; Darwiche, Hawraa; Blanco, Jesus; Gillenwater, Ann; Richards-Kortum, Rebecca; Tkaczyk, Tomasz S.
A multimodal endomicroscope was developed for cancer detection that combines hyperspectral and confocal imaging through a single foveated objective and a vibrating optical fiber bundle. Standard clinical examination has a limited ability to identify early stage oral cancer. Optical detection methods are typically restricted by either achievable resolution or a small field-of-view. By combining high resolution and widefield spectral imaging into a single probe, a device was developed that provides spectral and spatial information over a 5 mm field to locate suspicious lesions that can then be inspected in high resolution mode. The device was evaluated on ex vivo biopsies of human oral tumors.
Development of a universal, tunable, miniature fluorescence microscope for use at the point of care
(The Optical Society, 2018) Wong, Cynthia; Pawlowski, Michal E.; Forcucci, Alessandra; Majors, Catherine E.; Richards-Kortum, Rebecca; Tkaczyk, Tomasz S.
Fluorescence microscopy can be a powerful tool for cell-based diagnostic assays; however, imaging can be time consuming and labor intensive to perform. Tunable systems give the ability to electronically focus at user selected depths inside an object volume and may simplify the opto-mechanical design of the imaging system. We present a prototype of a universal, tunable, miniature fluorescence microscope built from poly(methyl methacrylate) singlets that incorporates miniature, electrowetted lenses for electronic focusing. We demonstrate the ability of this system to perform clinically relevant differential white blood cell counts using single use custom cartridges pre-loaded with the fluorescent dye acridine orange.
Development of Hyperspectral Imagers for Snapshot Optical Coherence Tomography
(2014-04-25) Nguyen, Thuc-Uyen; Tkaczyk, Tomasz S.; Richards-Kortum, Rebecca Rae; Baraniuk, Richard G.; Pierce, Mark C
Optical Coherence Tomography (OCT) is an established interferometry-based technique for volumetric tissue imaging with micrometer resolution, best known in many medical applications such as ophthalmologic imaging and endoscopy. Several clinically recognized examples include retinal imaging to detect glaucoma and age-related macular degeneration (AMD) or cardiovascular imaging when employed with a catheter. Scanning mechanism presenting in all current OCT technology requires moving parts, often limiting the system’s compactness, compromising light throughput and risking unwanted movement. Snapshot imaging thus allows fast and high-throughput acquisition while minimizing motion artifacts caused by instrumental vibration or samples’ transient nature. This thesis presents novel work contributing to the development of a snapshot 3-Dimensional OCT (3D-OCT) system. With theoretical and experimental evaluations, different hyperspectral imaging designs were surveyed to provide enhancements such as high throughput, dense spectral sampling, high sensitivity toward the appropriate spectrum and spatial-spectral tunability. A proof-of-concept snapshot 3D-OCT system is introduced to simultaneously collect signals of a volumetric datacube, enabling cellular visualization of scattering biological samples. This system affords diffraction-limited performance with reduced motion and requires minimal computational time.
Development of Image Mapping Spectrometer (IMS) for hyperspectral microscopy
(2011) Gao, Liang; Tkaczyk, Tomasz S.
A snapshot hyperspectral imaging device - Image Mapping Spectrometer (IMS) - has been developed for hyperspectral microscopy. The IMS replaces the camera in a digital imaging system, allowing one to add high speed snapshot spectrum acquisition capability to a variety of imaging modalities, e.g. microscopy, endoscopy, macroscopic imaging, to maximize the collection speed. The IMS described in this thesis is a parallel acquisition instrument that captures a hyperspectral datacube without scanning. It also allows" full" light throughput across the whole spectral collection range due to its snapshot operating format. The developments of three generations of the IMS (low sampling prototype, high sampling IMS, ruggedized IMS)have been reported in this thesis. Two illumination methods (filterless full-spectrum and structured illumination) are also developed for the IMS to achieve specific imaging aims. To show the application of the IMS in realtime hyperspectral imaging of live cells, the Calcium and a FRET-based biosensor are monitored simultaneously in ,B-cell dynamics. The imaging results demonstrate that the IMS has become an important spectral imaging modality in the biological imaging applications.
Development of image mapping spectrometer (IMS) for hyperspectral fluorescence microscopy
(2010) Gao, Liang; Tkaczyk, Tomasz S.
An image mapping spectrometer (IMS) for microscopy applications is presented. Its principle is based on the redirecting of image zones by specially organized thin mirrors within a custom fabricated component termed an image mapper. The demonstrated prototype can simultaneously acquire a 140nm spectral range within its 2D field of view from a single image. The spectral resolution of the system is 5.6nm. The FOV and spatial resolution of the IMS depend on the selected microscope objective and for the results presented is 45x45mu 2 and 0.45mum respectively. The system requires no scanning and minimal post data processing. In addition, the reflective nature of the image mapper and use of prisms for spectral dispersion make the system light efficient. Both of the above features are highly valuable for real time fluorescent-spectral imaging in biological and diagnostic applications.
Development of Miniature Objectives for Clinical Applications
(2021-04-30) Jeon, Hamin; Tkaczyk, Tomasz S.
Over the years, the most significant challenges for designing endomicroscopic objectives involved balancing between practical operational parameters. These parameters have included numerical aperture/resolution, field of view, working distance, and outer diameter of an objective. In addition, many applications nowadays use laser as a light source, for which, materials considered in the systems need to be carefully chosen. This dissertation focuses on addressing two specific issues to expand the capabilities of miniature microscopic objectives: (a) maximizing field (critical in clinical applications) while imaging at high resolution and (b) analyzing material properties that are critical in non-linear imaging and developing technologies specific to such materials. Two example system designs were developed to address these challenges. This dissertation describes spectrally encoded detection with a miniature objective to maximize data content and sampling. The objective works in tandem with a coherent imaging bundle, but can be also used with scanning systems. I also present on the development of a crystal based miniature objective for non-linear microsurgery applications. Ultrafast laser microsurgery requires a miniature objective that can non-invasively deliver high power laser pulses with high precision and, to this end, an objective with high NA (0.5 NA) as well as CaF2 and ZnS lenses was developed. CaF2 has a low nonlinear absorption coefficient, which enables the objective to better withstand the high power laser pulses. The high refractive index of ZnS is beneficial for the design of an objective with challenging requirements such as high NA or small outer diameter. As part of the prototyping process for the crystal-based objective, I developed a fabrication protocol for CaF2 and ZnS materials using the single point diamond turning method, which can yield surfaces with optical quality. This aspect has a broader impact since both CaF2 and ZnS materials transmit light from the visible range to long-wave infrared spectral range and can be applied to a number of other imaging applications. As a finishing step, both prototyped systems’ performance was assessed; against an USAF resolution target and ex vivo tissue samples (spectrally encoded system), and by measuring the focal spot size (miniature objective for laser microsurgery). As a result of the assessment, both systems demonstrated results that met the expected performance.
Differentiating between live and deadﾠMycobacterium smegmatisﾠusing autofluorescence
(Elsevier, 2016) Wong, Cynthia; Ha, Ngan P.; Pawlowski, Michal E.; Graviss, Edward A.; Tkaczyk, Tomasz S.
While there have been research efforts to find faster and more efficient diagnostic techniques for tuberculosis (TB), it is equally important to monitor a patient's response to treatment over time, especially with the increasing prevalence of multi-drug resistant (MDR) and extensively-drug resistant (XDR) TB. Between sputum smear microscopy, culture, and GeneXpert, only culture can verify viability of mycobacteria. However, it may take up to six weeks to grow Mycobacterium tuberculosis (Mtb), during which time the patient may have responded to treatment or the mycobacteria are still viable because the patient has MDR or XDR TB. In both situations, treatment incurs increased patient costs and makes them more susceptible to host-drug effects such as liver damage. Coenzyme Factor 420 (F420) is a fluorescent coenzyme found naturally in mycobacteria, with an excitation peak around 420 nm and an emission peak around 470 nm. Using Mycobacterium smegmatis, we show that live and dead mycobacteria undergo different rates of photobleaching over a period of 2 min. These preliminary experiments suggest that the different photobleaching rates could be used to help monitor a patient's response to TB treatment. In future studies, we propose to describe these experiments with Mtb as both M. smegmatis and Mtb use F420.
Fabrication of a multifaceted mapping mirror using two-photon polymerization for a snapshot image mapping spectrometer
(Optica Publishing Group, 2023) Lu, Jiawei; Ng, Xue Wen; Piston, David; Tkaczyk, Tomasz S.
A design and fabrication technique for making high-precision and large-format multifaceted mapping mirrors is presented. The method is based on two-photon polymerization, which allows more flexibility in the mapping mirror design. The mirror fabricated in this paper consists of 36 2D tilted square pixels, instead of the continuous facet design used in diamond cutting. The paper presents a detailed discussion of the fabrication parameters and optimization process, with particular emphasis on the optimization of stitching defects by compensating for the overall tilt angle and reducing the printing field of view. The fabricated mirrors were coated with a thin layer of aluminum (93 nm) using sputter coating to enhance the reflection rate over the target wave range. The mapping mirror was characterized using a white light interferometer and a scanning electron microscope, which demonstrates its optical quality surface (with a surface roughness of 12 nm) and high-precision tilt angles (with an average of 2.03% deviation). Finally, the incorporation of one of the 3D printed mapping mirrors into an image mapping spectrometer prototype allowed for the acquisition of high-quality images of the USAF resolution target and bovine pulmonary artery endothelial cells stained with three fluorescent dyes, demonstrating the potential of this technology for practical applications.
Fabrication of optical components using a consumer-grade lithographic printer
(Optical Society of America, 2019) Berglund, Gregory D.; Tkaczyk, Tomasz S.; Tkaczyk, Tomasz S.
The ability to 3D print optical elements will greatly expand the accessibility of optical fabrication. Here, we report on two fabrication techniques for plano-convex lens files using a consumer-grade lithographic printer. Lenses were post-processed using a simple spin coating technique with the resin used in the printing process or by curing directly on glass concave lenses. Average RMS roughness values were between 13 and 28 nm and RMS wavefront deviations were between 0.297 and 0.374 wave for spin-coated lenses. The average roughness RMS for the glass-cured lenses was 6 nm and the average form RMS was 0.048 wave.
Fabrication of waveguide directional couplers using 2-photon lithography
(Optica Publishing Group, 2023) Flynn, Christopher; Cao, Haimu; Applegate, Brian E.; Tkaczyk, Tomasz S.
Advances in 2-photon lithography have enabled in-lab production of sub-micron resolution and millimeter scale 3D optical components. The potential complex geometries are well suited to rapid prototyping and production of waveguide structures, interconnects, and waveguide directional couplers, furthering future development and miniaturization of waveguide-based imaging technologies. System alignment is inherent to the 2-photon process, obviating the need for manual assembly and allowing precise micron scale waveguide geometries not possible in traditional fused fiber coupler fabrication. Here we present the use of 2-photon lithography for direct printing of multi-mode waveguide couplers with air cladding and single mode waveguide couplers with uncured liquid photoresin cladding. Experimental results show reproducible coupling which can be modified by selected design parameters.
High performance image mapping spectrometer (IMS) for snapshot hyperspectral imaging applications
(Optical Society of America, 2019) Pawlowski, Michal E.; Dwight, Jason G.; Nguyen, Thuc-Uyen; Tkaczyk, Tomasz S.
A high performance, snapshot Image Mapping Spectrometer was developed that provides fast image acquisition (100 Hz) of 16 bit hyperspectral data cubes (210x210x46) over a spectral range of 515-842 nm. Essential details of the opto-mechanical design are presented. Spectral accuracy, precision, and image reconstruction metrics such as resolution are discussed. Fluorescently stained cell samples were used to directly compare the data obtained using newly developed and the reference image mapping spectrometer. Additional experimental results are provided to demonstrate the abilities of the new spectrometer to acquire highly-resolved, motion-artifact-free hyperspectral images at high temporal sampling rates.
High resolution microendoscopy for quantitative diagnosis of esophageal neoplasia
(2013-09-16) Shin, Dong Suk; Richards-Kortum, Rebecca Rae; Tkaczyk, Tomasz S.; Baraniuk, Richard G.; Anandasabapathy, Sharmila
Esophageal cancer is the eighth most common cancer in the world. Cancers of the esophagus account for 3.8% of all cases of cancers, with approximately 482,300 new cases reported in 2008 worldwide. In the United States alone, it is estimated that approximately 18,000 new cases will be diagnosed in 2013, and 15,210 deaths are expected. Despite advances in surgery and chemoradiation therapy, these advances have not led to a significant increase in survival rates, primarily because diagnosis often at an advanced and incurable stage when treatment is more difficult and less successful. Accurate, objective methods for early detection of esophageal neoplasia are needed. Here, quantitative classification algorithms for high resolution miscroendoscopic images were developed to distinguish between esophageal neoplastic and non-neoplastic tissue. A clinical study in 177 patients with esophageal squamous cell carcinoma (ESCC) was performed to evaluate the diagnostic performance of the classification algorithm in collaboration with the Mount Sinai Medical Center in the United States, the First Hospital of Jilin University in China, and the Cancer Institute and Hospital, the Chinese Academy of Medical Science in China. The study reported a sensitivity and specificity of 93% and 92%, respectively, in the training set, 87% and 97%, respectively, in the test set, and 84% and 95%, respectively, in an independent validation set. Another clinical study in 31 patients with Barrett’s esophagus resulted in a sensitivity of 84% and a specificity of 85%. Finally, a compact, portable version of the high resolution microendoscopy (HRME) device using a consumer-grade camera was developed and a series of biomedical experimental studies were carried out to assess the capability of the device.

Browsing by Author "Tkaczyk, Tomasz S."

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