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Rare-earth tritellurides (RTe3) are two-dimensional materials with unique quantum properties, ideal for investigating quantum phenomena and applications in supercapacitors, spintronics, and twistronics. This dissertation examines the electronic, magnetic, and phononic properties of the RTe3 family, exploring how these can be controlled using chemical pressure, cationic alloying, and external pressure.The impact of chemical pressure on RTe3 phononic properties was investigated through noninvasive micro-Raman spectroscopy, demonstrating the potential of optical measurements for determining charge density wave (CDW) transition temperatures. Cationic alloying studies showed seamless tuning of CDW transition temperatures by modifying lattice constants and revealed complex magnetism in alloyed RTe3 with multiple magnetic transitions.
A comprehensive external pressure study examined the influence of spacing between RTe3 layers on phononic and CDW properties across the RTe3 family. Comparisons between different RTe3 materials showed LaTe3, with the largest thermodynamic equilibrium interlayer spacing (smallest chemical pressure), has the most stable CDW phases at high pressures. Conversely, CDW phases in late RTe3 systems with larger internal chemical pressures were more easily suppressed by applied pressure.
The dissertation also investigated Schottky barrier realignment at RTe3/semiconductor interfaces induced by CDW transitions, revealing changes in Schottky barrier height and ideality factor around the CDW transition temperature. This indicates that chemical potential changes of RTe3 below the CDW transition temperature influence Schottky junction properties, enabling CDW state probing through interface property measurements.
A detailed experimental and theoretical analysis of the oxidation process of RTe3 compounds was performed, which revealed faster degradation in late RTe3 systems. Electronic property changes, like CDW transition temperature and chemical potential, are observed as degradation progresses. Quantum mechanical simulations suggested that degradation primarily results from strong oxidizing reactions with O2 molecules, while humidity (H2O) plays a negligible role unless Te vacancies exist.
Lastly, the dissertation establishes a large-area thin film deposition at relatively low temperatures using a soft sputtering technique. While focused on MoTe2 deposition, this technique may also apply to RTe3 thin film deposition.
Overall, this dissertation expands the understanding of the fundamental properties of RTe3 materials and lays the groundwork for potential device applications.
ContributorsYumigeta, Kentaro (Author) / Tongay, Sefaattin (Thesis advisor) / Ponce, Fernando (Committee member) / Drucker, Jeffery (Committee member) / Erten, Onur (Committee member) / Arizona State University (Publisher)
Created2023
Description
APOE encodes for a lipid transport protein and has three allelic variants-APOE ε2, ε3 and ε4 each of which differentially modulate the risk for Alzheimer’s disease (AD). The presence of the ε4 allele of APOE greatly increases AD risk compared to the presence of the more prevalent and risk neutral ε3 allele. An imbalance in the generation and clearance of amyloid beta (Aβ) peptides has been hypothesized to play a key role in driving the disease. APOE4 impacts several AD-relevant cellular processes. However, it is unclear whether these effects represent a gain of toxic function or a loss of function, specifically as it relates to modulating amyloid beta (Aβ) levels. Here, a set of APOE knockout (KO) and APOE4 isogenic human induced pluripotent stem cells (hiPSCs) were generated from a parental APOE3 hiPSC line with a highly penetrant familial AD (fAD) mutation to investigate this with respect to Aβ secretion in neural cultures and Aβ uptake in monocultures of microglia-like cells (iMGLs). Conversion of APOE3 to E4 as well as functionally knocking APOE out from the APOE3 parental line, result in elevated Aβ levels in neural cultures, likely through multiple mechanisms including the altered processing of the precursor protein to Aβ called amyloid precursor protein (APP). In pure neuronal cultures, a shift in the processing of APP was observed with the Aβ-generating amyloidogenic pathway being favored in both APOE3 as well as APOE4 neurons compared to APOE KO neurons, with APOE4 neurons exhibiting a greater shift. In iMGLs derived from the isogenic hiPSC lines, expression of APOE, regardless of the isoform, lowered the uptake of Aβ. Overall, APOE4 modulates Aβ levels through distinct loss of protective and gain of function effects. Dissecting these effects would contribute towards a better understanding of the design of potential APOE-targeted therapeutics in the future.
ContributorsRajaram Srinivasan, Gayathri (Author) / Brafman, David (Thesis advisor) / Plaisier, Christopher (Committee member) / Newbern, Jason (Committee member) / Stabenfeldt, Sarah (Committee member) / Wang, Xiao (Committee member) / Arizona State University (Publisher)
Created2024
Description
Janus Transition Metal Dichalcogenides (TMDs) are emerging 2D quantum materials with an asymmetric chalcogen configuration that induces an out-of-plane dipole moment. Their synthesis has been a limiting factor in exploring these systems' many-body physics and interactions. This dissertation examines the challenges associated with synthesis and charts the excitonic landscape of Janus crystals by proposing the development of the Selective Epitaxy and Atomic Replacement (SEAR) technique. SEAR utilizes ionized radical precursors to modify TMD monolayers into their Janus counterparts selectively. The synthesis is coupled with optical spectroscopy and monitored in real-time, enabling precise control of reaction kinetics and the structural evolution of Janus TMDs. The results demonstrate the synthesis of Janus TMDs at ambient temperatures, reducing defects and preserving the structural integrity with the hitherto best-reported exciton linewidth emission value, indicating ultra-high optical quality. Cryogenic optical spectroscopy (4K) coupled with a magnetic field on Janus monolayers has allowed the isolation of excitonic transitions and the identification of charged exciton complexes. Further study into macroscopic and microscopic defects reveals that structural asymmetry results in the spontaneous formation of 2D Janus Nanoscrolls from an in-plane strain. The chalcogen arrangement in these structures dictates two types of scrolling dynamics that form Archimedean or inverted C-scrolls. High-resolution scanning transmission electron microscopy of these superlattices shows a preferential orientation of scrolling and formation of Moiré patterns. These materials' thermodynamically favorable defect states are identified and shown to be optically active. The encapsulation of Janus TMDs with hexagonal Boron Nitride (h-BN) has allowed isolation defect transitions. DFT coupled with power-dependent PL spectroscopy at 4K shows the broad defect band to be a convolution of individual defect states with extremely narrow linewidth (2 meV) indicative of a two-state quantum system. The research presents a comprehensive synthesis approach with insights into the structural and morphological stability of 2D Janus layers, establishing a complete structure-property correlation of optical transitions and defect states, broadening the scope for practical applications in quantum information technologies.
ContributorsSayyad, Mohammed Yasir (Author) / Tongay, Sefaattin (Thesis advisor) / Esqueda, Ivan S (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2024
Description
Recently, two-dimensional (2D) materials have emerged as a new class of materials with highly attractive electronic, optical, magnetic, and thermal properties. However, there exists a sub-category of 2D layers wherein constituent metal atoms are arranged in a way that they form weakly coupled chains confined in the 2D landscape. These weakly coupled chains extend along particular lattice directions and host highly attractive properties including high thermal conduction pathways, high-mobility carriers, and polarized excitons. In a sense, these materials offer a bridge between traditional one-dimensional (1D) materials (nanowires and nanotubes) and 2D layered systems. Therefore, they are often referred as pseudo-1D materials, and are anticipated to impact photonics and optoelectronics fields.
This dissertation focuses on the novel growth routes and fundamental investigation of the physical properties of pseudo-1D materials. Example systems are based on transition metal chalcogenide such as rhenium disulfide (ReS2), titanium trisulfide (TiS3), tantalum trisulfide (TaS3), and titanium-niobium trisulfide (Nb(1-x)TixS3) ternary alloys. Advanced growth, spectroscopy, and microscopy techniques with density functional theory (DFT) calculations have offered the opportunity to understand the properties of these materials both experimentally and theoretically. The first controllable growth of ReS2 flakes with well-defined domain architectures has been established by a state-of-art chemical vapor deposition (CVD) method. High-resolution electron microscopy has offered the very first investigation into the structural pseudo-1D nature of these materials at an atomic level such as the chain-like features, grain boundaries, and local defects.
Pressure-dependent Raman spectroscopy and DFT calculations have investigated the origin of the Raman vibrational modes in TiS3 and TaS3, and discovered the unusual pressure response and its effect on Raman anisotropy. Interestingly, the structural and vibrational anisotropy can be retained in the Nb(1-x)TixS3 alloy system with the presence of phase transition at a nominal Ti alloying limit. Results have offered valuable experimental and theoretical insights into the growth routes as well as the structural, optical, and vibrational properties of typical pseudo-1D layered systems. The overall findings hope to shield lights to the understanding of this entire class of materials and benefit the design of 2D electronics and optoelectronics.
This dissertation focuses on the novel growth routes and fundamental investigation of the physical properties of pseudo-1D materials. Example systems are based on transition metal chalcogenide such as rhenium disulfide (ReS2), titanium trisulfide (TiS3), tantalum trisulfide (TaS3), and titanium-niobium trisulfide (Nb(1-x)TixS3) ternary alloys. Advanced growth, spectroscopy, and microscopy techniques with density functional theory (DFT) calculations have offered the opportunity to understand the properties of these materials both experimentally and theoretically. The first controllable growth of ReS2 flakes with well-defined domain architectures has been established by a state-of-art chemical vapor deposition (CVD) method. High-resolution electron microscopy has offered the very first investigation into the structural pseudo-1D nature of these materials at an atomic level such as the chain-like features, grain boundaries, and local defects.
Pressure-dependent Raman spectroscopy and DFT calculations have investigated the origin of the Raman vibrational modes in TiS3 and TaS3, and discovered the unusual pressure response and its effect on Raman anisotropy. Interestingly, the structural and vibrational anisotropy can be retained in the Nb(1-x)TixS3 alloy system with the presence of phase transition at a nominal Ti alloying limit. Results have offered valuable experimental and theoretical insights into the growth routes as well as the structural, optical, and vibrational properties of typical pseudo-1D layered systems. The overall findings hope to shield lights to the understanding of this entire class of materials and benefit the design of 2D electronics and optoelectronics.
ContributorsWu, Kedi (Author) / Tongay, Sefaattin (Thesis advisor) / Zhuang, Houlong (Committee member) / Green, Matthew (Committee member) / Arizona State University (Publisher)
Created2018
Description
There has been a surge in two-dimensional (2D) materials field since the discovery of graphene in 2004. Recently, a new class of layered atomically thin materials that exhibit in-plane structural anisotropy, such as black phosphorous, transition metal trichalcogenides and rhenium dichalcogenides (ReS2), have attracted great attention. The reduced symmetry in these novel 2D materials gives rise to highly anisotropic physical properties that enable unique applications in next-gen electronics and optoelectronics. For example, higher carrier mobility along one preferential crystal direction for anisotropic field effect transistors and anisotropic photon absorption for polarization-sensitive photodetectors.
This dissertation endeavors to address two key challenges towards practical application of anisotropic materials. One is the scalable production of high quality 2D anisotropic thin films, and the other is the controllability over anisotropy present in synthesized crystals. The investigation is focused primarily on rhenium disulfide because of its chemical similarity to conventional 2D transition metal dichalcogenides and yet anisotropic nature. Carefully designed vapor phase deposition has been demonstrated effective for batch synthesis of high quality ReS2 monolayer. Heteroepitaxial growth proves to be a feasible route for controlling anisotropic directions. Scanning/transmission electron microscopy and angle-resolved Raman spectroscopy have been extensively applied to reveal the structure-property relationship in synthesized 2D anisotropic layers and their heterostructures.
This dissertation endeavors to address two key challenges towards practical application of anisotropic materials. One is the scalable production of high quality 2D anisotropic thin films, and the other is the controllability over anisotropy present in synthesized crystals. The investigation is focused primarily on rhenium disulfide because of its chemical similarity to conventional 2D transition metal dichalcogenides and yet anisotropic nature. Carefully designed vapor phase deposition has been demonstrated effective for batch synthesis of high quality ReS2 monolayer. Heteroepitaxial growth proves to be a feasible route for controlling anisotropic directions. Scanning/transmission electron microscopy and angle-resolved Raman spectroscopy have been extensively applied to reveal the structure-property relationship in synthesized 2D anisotropic layers and their heterostructures.
ContributorsChen, Bin, 1968- (Author) / Tongay, Sefaattin (Thesis advisor) / Bertoni, Mariana (Committee member) / Chang, Lan-Yun (Committee member) / Arizona State University (Publisher)
Created2018
Description
Layer structured two dimensional (2D) semiconductors have gained much interest due to their intriguing optical and electronic properties induced by the unique van der Waals bonding between layers. The extraordinary success for graphene and transition metal dichalcogenides (TMDCs) has triggered a constant search for novel 2D semiconductors beyond them. Gallium chalcogenides, belonging to the group III-VI compounds, are a new class of 2D semiconductors that carry a variety of interesting properties including wide spectrum coverage of their bandgaps and thus are promising candidates for next generation electronic and optoelectronic devices. Pushing these materials toward applications requires more controllable synthesis methods and facile routes for engineering their properties on demand.
In this dissertation, vapor phase transport is used to synthesize layer structured gallium chalcogenide nanomaterials with highly controlled structure, morphology and properties, with particular emphasis on GaSe, GaTe and GaSeTe alloys. Multiple routes are used to manipulate the physical properties of these materials including strain engineering, defect engineering and phase engineering. First, 2D GaSe with controlled morphologies is synthesized on Si(111) substrates and the bandgap is significantly reduced from 2 eV to 1.7 eV due to lateral tensile strain. By applying vertical compressive strain using a diamond anvil cell, the band gap can be further reduced to 1.4 eV. Next, pseudo-1D GaTe nanomaterials with a monoclinic structure are synthesized on various substrates. The product exhibits highly anisotropic atomic structure and properties characterized by high-resolution transmission electron microscopy and angle resolved Raman and photoluminescence (PL) spectroscopy. Multiple sharp PL emissions below the bandgap are found due to defects localized at the edges and grain boundaries. Finally, layer structured GaSe1-xTex alloys across the full composition range are synthesized on GaAs(111) substrates. Results show that GaAs(111) substrate plays an essential role in stabilizing the metastable single-phase alloys within the miscibility gaps. A hexagonal to monoclinic phase crossover is observed as the Te content increases. The phase crossover features coexistence of both phases and isotropic to anisotropic structural transition.
Overall, this work provides insights into the controlled synthesis of gallium chalcogenides and opens up new opportunities towards optoelectronic applications that require tunable material properties.
In this dissertation, vapor phase transport is used to synthesize layer structured gallium chalcogenide nanomaterials with highly controlled structure, morphology and properties, with particular emphasis on GaSe, GaTe and GaSeTe alloys. Multiple routes are used to manipulate the physical properties of these materials including strain engineering, defect engineering and phase engineering. First, 2D GaSe with controlled morphologies is synthesized on Si(111) substrates and the bandgap is significantly reduced from 2 eV to 1.7 eV due to lateral tensile strain. By applying vertical compressive strain using a diamond anvil cell, the band gap can be further reduced to 1.4 eV. Next, pseudo-1D GaTe nanomaterials with a monoclinic structure are synthesized on various substrates. The product exhibits highly anisotropic atomic structure and properties characterized by high-resolution transmission electron microscopy and angle resolved Raman and photoluminescence (PL) spectroscopy. Multiple sharp PL emissions below the bandgap are found due to defects localized at the edges and grain boundaries. Finally, layer structured GaSe1-xTex alloys across the full composition range are synthesized on GaAs(111) substrates. Results show that GaAs(111) substrate plays an essential role in stabilizing the metastable single-phase alloys within the miscibility gaps. A hexagonal to monoclinic phase crossover is observed as the Te content increases. The phase crossover features coexistence of both phases and isotropic to anisotropic structural transition.
Overall, this work provides insights into the controlled synthesis of gallium chalcogenides and opens up new opportunities towards optoelectronic applications that require tunable material properties.
ContributorsCai, Hui, Ph.D (Author) / Tongay, Sefaattin (Thesis advisor) / Dwyer, Christian (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2018
Description
Synthetic manipulation of chromatin dynamics has applications for medicine, agriculture, and biotechnology. However, progress in this area requires the identification of design rules for engineering chromatin systems. In this thesis, I discuss research that has elucidated the intrinsic properties of histone binding proteins (HBP), and apply this knowledge to engineer novel chromatin binding effectors. Results from the experiments described herein demonstrate that the histone binding domain from chromobox protein homolog 8 (CBX8) is portable and can be customized to alter its endogenous function. First, I developed an assay to identify engineered fusion proteins that bind histone post translational modifications (PTMs) in vitro and regulate genes near the same histone PTMs in living cells. This assay will be useful for assaying the function of synthetic histone PTM-binding actuators and probes. Next, I investigated the activity of a novel, dual histone PTM binding domain regulator called Pc2TF. I characterized Pc2TF in vitro and in cells and show it has enhanced binding and transcriptional activation compared to a single binding domain fusion called Polycomb Transcription Factor (PcTF). These results indicate that valency can be used to tune the activity of synthetic histone-binding transcriptional regulators. Then, I report the delivery of PcTF fused to a cell penetrating peptide (CPP) TAT, called CP-PcTF. I treated 2D U-2 OS bone cancer cells with CP-PcTF, followed by RNA sequencing to identify genes regulated by CP-PcTF. I also showed that 3D spheroids treated with CP-PcTF show delayed growth. This preliminary work demonstrated that an epigenetic effector fused to a CPP can enable entry and regulation of genes in U-2 OS cells through DNA independent interactions. Finally, I described and validated a new screening method that combines the versatility of in vitro transcription and translation (IVTT) expressed protein coupled with the histone tail microarrays. Using Pc2TF as an example, I demonstrated that this assay is capable of determining binding and specificity of a synthetic HBP. I conclude by outlining future work toward engineering HBPs using techniques such as directed evolution and rational design. In conclusion, this work outlines a foundation to engineer and deliver synthetic chromatin effectors.
ContributorsTekel, Stefan (Author) / Haynes, Karmella (Thesis advisor) / Mills, Jeremy (Committee member) / Caplan, Michael (Committee member) / Brafman, David (Committee member) / Arizona State University (Publisher)
Created2019
Description
Nanoporous materials, with pore sizes less than one nanometer, have been incorporated as filler materials into state-of-the-art polyamide-based thin-film composite membranes to create thin-film nanocomposite (TFN) membranes for reverse osmosis (RO) desalination. However, these TFN membranes have inconsistent changes in desalination performance as a result of filler incorporation. The nano-sized filler’s transport role for enhancing water permeability is unknown: specifically, there is debate around the individual transport contributions of the polymer, nanoporous particle, and polymer/particle interface. Limited studies exist on the pressure-driven water transport mechanism through nanoporous single-crystal nanoparticles. An understanding of the nanoporous particles water transport role in TFN membranes will provide a better physical insight on the improvement of desalination membranes.
This dissertation investigates water permeation through single-crystal molecular sieve zeolite A particles in TFN membranes in four steps. First, the meta-analysis of nanoporous materials (e.g., zeolites, MOFs, and graphene-based materials) in TFN membranes demonstrated non-uniform water-salt permselectivity performance changes with nanoporous fillers. Second, a systematic study was performed investigating different sizes of non-porous (pore-closed) and nanoporous (pore-opened) zeolite particles incorporated into conventionally polymerized TFN membranes; however, the challenges of particle aggregation, non-uniform particle dispersion, and possible particle leaching from the membranes limit analysis. Third, to limit aggregation and improve dispersion on the membrane, a TFN-model membrane synthesis recipe was developed that immobilized the nanoparticles onto the support membranes surface before the polymerization reaction. Fourth, to quantify the possible water transport pathways in these membranes, two different resistance models were employed.
The experimental results show that both TFN and TFN-model membranes with pore-opened particles have higher water permeance compared to those with pore-closed particles. Further analysis using the resistance in parallel and hybrid models yields that water permeability through the zeolite pores is smaller than that of the particle/polymer interface and higher than the water permeability of the pure polymer. Thus, nanoporous particles increase water permeability in TFN membranes primarily through increased water transport at particle/polymer interface. Because solute rejection is not significantly altered in our TFN and TFN-model systems, the results reveal that local changes in the polymer region at the polymer/particle interface yield high water permeability.
This dissertation investigates water permeation through single-crystal molecular sieve zeolite A particles in TFN membranes in four steps. First, the meta-analysis of nanoporous materials (e.g., zeolites, MOFs, and graphene-based materials) in TFN membranes demonstrated non-uniform water-salt permselectivity performance changes with nanoporous fillers. Second, a systematic study was performed investigating different sizes of non-porous (pore-closed) and nanoporous (pore-opened) zeolite particles incorporated into conventionally polymerized TFN membranes; however, the challenges of particle aggregation, non-uniform particle dispersion, and possible particle leaching from the membranes limit analysis. Third, to limit aggregation and improve dispersion on the membrane, a TFN-model membrane synthesis recipe was developed that immobilized the nanoparticles onto the support membranes surface before the polymerization reaction. Fourth, to quantify the possible water transport pathways in these membranes, two different resistance models were employed.
The experimental results show that both TFN and TFN-model membranes with pore-opened particles have higher water permeance compared to those with pore-closed particles. Further analysis using the resistance in parallel and hybrid models yields that water permeability through the zeolite pores is smaller than that of the particle/polymer interface and higher than the water permeability of the pure polymer. Thus, nanoporous particles increase water permeability in TFN membranes primarily through increased water transport at particle/polymer interface. Because solute rejection is not significantly altered in our TFN and TFN-model systems, the results reveal that local changes in the polymer region at the polymer/particle interface yield high water permeability.
ContributorsCay Durgun, Pinar (Author) / Lind, Mary Laura (Thesis advisor) / Lin, Jerry Y. S. (Committee member) / Green, Matthew D. (Committee member) / Seo, Dong K. (Committee member) / Tongay, Sefaattin (Committee member) / Arizona State University (Publisher)
Created2018
Description
Neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, or amyotrophic lateral sclerosis are defined by the loss of several types of neurons and glial cells within the central nervous system (CNS). Combatting these diseases requires a robust population of relevant cell types that can be employed in cell therapies, drug screening, or patient specific disease modeling. Human induced pluripotent stem cells (hiPSC)-derived neural progenitor cells (hNPCs) have the ability to self-renew indefinitely and differentiate into the various neuronal and glial cell types of the CNS. In order to realize the potential of hNPCs, it is necessary to develop a xeno-free scalable platform for effective expansion and differentiation. Previous work in the Brafman lab led to the engineering of a chemically defined substrate—vitronectin derived peptide (VDP), which allows for the long-term expansion and differentiation of hNPCs. In this work, we use this substrate as the basis for a microcarrier (MC)-based suspension culture system. Several independently derived hNPC lines were cultured on MCs for multiple passages as well as efficiently differentiated to neurons. Finally, this MC-based system was used in conjunction with a low shear rotating wall vessel (RWV) bioreactor for the integrated, large-scale expansion and neuronal differentiation of hNPCs. Finally, VDP was shown to support the differentiation of hNPCs into functional astrocytes. Overall, this fully defined and scalable biomanufacturing system will facilitate the generation of hNPCs and their derivatives in quantities necessary for basic and translational applications.
ContributorsMorgan, Daylin (Author) / Brafman, David (Thesis advisor) / Stabenfeldt, Sarah (Committee member) / Wang, Xiao (Committee member) / Arizona State University (Publisher)
Created2018
Description
Calcium imaging is a well-established, non-invasive or minimally technique designed to study the electrical signaling neurons. Calcium regulates the release of gliotransmitters in astrocytes. Analyzing astrocytic calcium transients can provide significant insights into mechanisms such as neuroplasticity and neural signal modulation.
In the past decade, numerous methods have been developed to analyze in-vivo calcium imaging data that involves complex techniques such as overlapping signals segregation and motion artifact correction. The hypothesis used to detect calcium signal is the spatiotemporal sparsity of calcium signal, and these methods are unable to identify the passive cells that are not actively firing during the time frame in the video. Statistics regarding the percentage of cells in each frame of view can be critical for the analysis of calcium imaging data for human induced pluripotent stem cells derived neurons and astrocytes.
The objective of this research is to develop a simple and efficient semi-automated pipeline for analysis of in-vitro calcium imaging data. The region of interest (ROI) based image segmentation is used to extract the data regarding intensity fluctuation caused by calcium concentration changes in each cell. It is achieved by using two approaches: basic image segmentation approach and a machine learning approach. The intensity data is evaluated using a custom-made MATLAB that generates statistical information and graphical representation of the number of spiking cells in each field of view, the number of spikes per cell and spike height.
In the past decade, numerous methods have been developed to analyze in-vivo calcium imaging data that involves complex techniques such as overlapping signals segregation and motion artifact correction. The hypothesis used to detect calcium signal is the spatiotemporal sparsity of calcium signal, and these methods are unable to identify the passive cells that are not actively firing during the time frame in the video. Statistics regarding the percentage of cells in each frame of view can be critical for the analysis of calcium imaging data for human induced pluripotent stem cells derived neurons and astrocytes.
The objective of this research is to develop a simple and efficient semi-automated pipeline for analysis of in-vitro calcium imaging data. The region of interest (ROI) based image segmentation is used to extract the data regarding intensity fluctuation caused by calcium concentration changes in each cell. It is achieved by using two approaches: basic image segmentation approach and a machine learning approach. The intensity data is evaluated using a custom-made MATLAB that generates statistical information and graphical representation of the number of spiking cells in each field of view, the number of spikes per cell and spike height.
ContributorsBhandarkar, Siddhi Umesh (Author) / Brafman, David (Thesis advisor) / Stabenfeldt, Sarah (Committee member) / Tian, Xiaojun (Committee member) / Arizona State University (Publisher)
Created2019