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Recent Submissions

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    Developments in Photon Absorption Remote Sensing Microscopy and Deep Learning–Based Virtual Histochemical Staining
    (University of Waterloo, 2026-03-11) Tweel, James
    Histological staining remains the gold standard of diagnostic pathology, enabling visualization of tissue structure and cellular morphology. However, traditional staining workflows are time-consuming, destructive, and chemically intensive, limiting the number of stains that can be applied to valuable biopsy samples. These processes also introduce delays, variability in stain quality, and high resource demands. To address these limitations, this thesis presents a label-free histology framework that combines Photon Absorption Remote Sensing (PARS) microscopy with deep learning–based virtual staining to replicate commonly used histochemical stains without altering or consuming the tissue. The first component of this work focuses on the development of an automated whole slide PARS system designed for imaging thin, transmissible tissue sections. The system captures sub-micron resolution radiative and non-radiative absorption contrasts using 266 nm UV excitation, targeting endogenous chromophores such as DNA and extracellular matrix components to reveal nuclear and connective tissue structures. Whole slide imaging is achieved through automated focusing, tiling, and contrast leveling, producing gigapixel-scale images directly comparable to standard hematoxylin and eosin (H&E) slides. The second component introduces a deep learning virtual staining pipeline based on the unpaired CycleGAN architecture, with direct comparison to the paired Pix2Pix model. These models are trained on one-to-one whole slide images of PARS data and chemically stained H&E slides. The first masked clinical concordance study is conducted using breast needle core biopsies, where board-certified pathologists independently diagnose and assess the virtual and real H&E slides. The study demonstrates substantial diagnostic agreement, validating the clinical viability of the PARS-based virtual staining approach. The final component expands the PARS imaging system through the integration of a secondary long-wave UV excitation wavelength (355 nm), enabling sensitivity to additional biomolecular absorbers and thereby expanding the captured label-free contrasts. The additional label-free contrast contributes to improved emulation of histochemical stains beyond H&E, including Masson’s Trichrome, Periodic acid–Schiff, and Jones methenamine silver. To further improve performance, a more advanced registration-guided GAN model (RegGAN) is adopted, outperforming both Pix2Pix and CycleGAN. The resulting whole slide virtual images closely match their ground truth counterparts in qualitative appearance, quantitative metrics, and masked pathology review. Together, this work presents a non destructive histology pipeline capable of generating high-resolution, multi-stain images of commonly used stains without chemical labeling, representing a step toward integrating label-free microscopy and deep learning virtual staining into routine pathology workflows.
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    Transport and Irreversible Retention of Hydrophobic Nanoparticles by Fluid-fluid and Fluid-Solid Interfaces in Porous Media
    (University of Waterloo, 2026-03-06) Rahham, Youssra
    Hydrophobic nanoparticle (NP) transport in porous media has implications for aquifer transport and retention of a wide range of contaminants that infiltrate water resources and threaten human health as well as aquatic environments. Comprehension of NP transport and interactions with hydrophobic surfaces and interfaces -given their ubiquity in porous aquifers- is essential for groundwater remediation from organic contaminants, toxic engineered NPs, and nanoplastics. This research investigates the transport and attachment of hydrophobic NPs under varying physicochemical conditions in saturated and unsaturated porous media by integrating experimental observations across multiple scales, theoretical extended-DLVO predictions, and numerical modeling. A non-toxic, negatively-charged, hydrophobic model NP system synthesized from ethyl cellulose (EC), and exhaustively characterized for colloidal stability and interfacial interactions, was employed to systematically explore NP interactions with fluid-fluid and solid-fluid interfaces. The upscaling capability of an advection-dispersion-retention continuum model was compared vis-à-vis a pore network model of irreversible NP attachment onto fluid interfaces in 3D columns packed with spherical glass beads, showing that the latter captures key pore-scale dynamics such as bypassed interfaces, slow-moving corner flows, and diffusion-dominated retention. Transport experiments in 2D microfluidic pore networks confirm that the dynamics of NP retention in unsaturated porous media depend not only on the saturation of the non-wetting phase, but also on its connectivity and the accessibility of immobile fluid-fluid interfaces. Experimental evidence demonstrates that ethyl cellulose nanoparticles (EC-NPs) irreversibly attach onto immobile fluid-fluid interfaces and experience delay in slow moving zones owing to geometric effects. Similarly, hydrophobic solid-fluid interfaces represent permanent sinks for EC-NPs. The attraction between a hydrophobic particle and a hydrophobic solid surface may be strong enough for irreversible attachment to take place, even under conditions of strong electrostatic repulsion. The strength of this hydrophobic interaction between an EC-NP and a hydrophobic collector surface is demonstrated using octadecyltrichlorosilane-treated glass and quantified via systematic contact angle measurements. Under destabilizing ionic conditions, irreversible EC-NP aggregation results in the formation of a secondary porous structure within hydrophilic porous media, altering permeability and retention patterns. Both phenomena are inadequately captured by macroscopic breakthrough curve (BTC) analyses alone. For example, attachment onto fluid-fluid and fluid-solid interfaces manifests itself on BTCs at low injection concentrations, whereas the opposite effect emerges in the presence of salt. This research advances the field by conducting transport experiments under carefully controlled conditions. The findings, supported by theoretical analysis and supporting experimental evidence, highlight key limitations in current modeling approaches and provide foundational experimental data that should advance the development and validation of numerical models of nano-colloid transport in porous media. Besides enhancing predictive capabilities for the fate of hydrophobic nanomaterials in the subsurface, this research informs risk assessment and the design of groundwater remediation strategies, ex-situ (i.e., NP filtration media) and in-situ (e.g., permeable adsorptive barriers for fluorinated contaminant capture and oil spill cleanup).
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    Soft Matter Templating for Fabrication of Hierarchical Cryogels
    (University of Waterloo, 2026-03-06) Amirieh, Estatira
    Hierarchical cryogels are a promising class of lightweight, highly porous materials whose multiscale pore architecture can simultaneously enable rapid mass transport and high adsorption capacity, making them attractive for diverse applications. Numerous approaches have been introduced so far to produce hierarchical cryogels. However, these approaches are often processing-intensive, requiring multi-step templating, tightly controlled freezing protocols, or complex drying strategies that can limit scalability and restrict independent control over pore hierarchy. Moreover, most existing approaches rely on the fabrication of structured cryogels from gel-like precursors, which require high solid concentrations, thereby increasing density and compromising lightweight characteristics. This work utilizes a recently introduced technique by our group, namely liquid-streaming (templating), that facilitates the formation of hierarchical cellulose nanocrystal (CNC)-based cryogels through filamentary structuring of CNC aqueous suspension (liquid-like) in an apolar medium. In this approach, an aqueous nanomaterial dispersion is injected into a surfactant-containing hexane bath to produce a filamentous all-liquid network, which is subsequently freeze-dried to yield a worm-like hierarchical cryogel. A central objective of this approach is to simplify the rheological requirements, broaden the range of extrudable materials, and dissociate filament stability from bulk viscoelasticity. By controlling factors such as interfacial tension, interfacial rheological features, extrusion rate, and solid content, one can map the operational “printing window” for producing continuous, shape-persistent filaments even from low-viscosity fluids. Herein, key injection factors governing filament formation, including needle size, nanomaterial concentration, and injection pressure, are investigated to delineate the transition between stable filament formation and breakup behavior. It is also shown how these factors dictate the morphology, e.g., filament diameter, of the structured liquids. A process–structure map is developed to define operating windows that reliably produce filamentous all-liquid systems across a range of conditions, providing practical guidance for reproducible fabrication and architectural control. The resulting worm-like cryogels from the engineered filamentous all-liquid systems exhibit intrinsic hierarchical porosity, with macroporous inter-filament voids coupled with finer porosity on and within the filament structure. To evaluate functional implications of this architecture, worm-like cryogels are compared against conventional bulk cryogel counterparts in oil absorption testing. The worm-like cryogel demonstrates improved uptake performance, achieving a 22% increase in oil absorption efficiency relative to bulk structures. In general, this thesis establishes liquid templating as an accessible and tunable route to CNC-based hierarchical cryogels and provides processing guidelines that link injection conditions to structure and absorption performance.
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    Vibration Analysis of Cable-Harnessed Structures: Plate Optimal Wrapping and Cylindrical Shell Continuum Modeling
    (University of Waterloo, 2026-03-06) Oluyemi, Momoiyioluwa
    Cables are integral components of modern engineering systems, serving functions that range from transmitting electrical signals to bearing mechanical loads. Their widespread use in aerospace, automotive, civil, and marine applications has made it increasingly important to understand and predict their dynamic influence on host structures. In lightweight spacecraft components, where cables may account for a significant portion of the total mass, inaccurate modeling of cable-structure interactions can compromise control strategies and system reliability. This thesis advances the analytical modeling of cable-harnessed structures and explores optimal cable placement strategies that minimize their dynamic impact, thereby supporting the development of robust control frameworks for aerospace systems and beyond. The thesis can be classified as having two main areas of focus. The first area focuses on plate structures and the identification of optimal cable wrapping configurations that minimize the dynamic influence of cables on their host plates. An analytical homogenization-based framework is employed to evaluate zigzag and diagonal wrapping patterns, with configurations ranked according to how closely their frequency response functions align with those of bare plates. A detailed parametric study reveals specific wrapping geometries that yield negligible dynamic impact, offering practical strategies for simplifying structural models. These analytical predictions are validated through finite element simulations and experimental modal testing on fabricated specimens, confirming that certain cable arrangements can be implemented without significantly altering the host plate’s vibrational behavior. The combined analytical and experimental results provide a foundation for cable placement strategies that reduce modeling complexity and enhance vibration control in plate-like structures. The second area introduces the continuum modeling of cable-harnessed cylindrical shell structures. Building on prior work for beams and plates, analytical formulations are derived for shells with cables oriented axially and circumferentially. Using an energy-equivalence homogenization approach, coupled partial differential equations are obtained to describe the dynamic behavior of these systems. Parametric studies are conducted to assess the influence of cable orientation and geometric parameters, with results compared against finite element simulations to verify model fidelity. The findings demonstrate that circumferential cable placement exerts a significantly greater dynamic impact on the host shell than axial placement. This comparative insight highlights the critical role of cable orientation in shell dynamics and establishes a continuum modeling framework that can be extended to more complex cable-harnessed structures.
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    My name is Jon...without an 'H'
    (University of Waterloo, 2024) Ochana, Mary; Bredahl, Laura
    It’s time you started wondering about researcher identifiers! With the implementation of open access and research data management policies in Canada, we’re quickly learning that data integrity and consistency can get pretty messy. Persistent identifiers such as the Open Researcher and Contributor ID (ORCID) are an important part of ensuring consistent data workflows and can help with reliably matching authors to their institutions and their research outputs across systems. But many institutions are just starting to utilize ORCID because its utility is largely a mystery them. In this presentation we will demystify ORCID and persistent identifiers and discuss the benefits and challenges of implementing ORCID within a university. ORCID has the potential to help with automation and streamlining workflows using research information, increase data consistency and quality, and ultimately save time for research administration. Working with ORCID is a huge opportunity for research offices and libraries to collaborate and gain benefits for the whole institution. It’s time to learn about ORCID.