Ilya Valmianski

Automatic Identification of Fluorescently Labeled Brain Cells for Rapid Functional Imaging

The on-line identification of labeled cells and vessels is a rate-limiting step in scanning microscopy. We use supervised learning to formulate an algorithm that rapidly and automatically tags fluorescently labeled somata in full-field images of cortex and constructs an optimized scan path through these cells. A single classifier works across multiple subjects, regions of the cortex of similar depth, and different magnification and contrast levels without the need to retrain the algorithm. Retraining only has to be performed when the morphological properties of the cells change significantly. In conjunction with two-photon laser scanning microscopy and bulk-labeling of cells in layers 2/3 of rat parietal cortex with a calcium indicator, we can automatically identify ∼ 50 cells within 1 min and sample them at ∼ 100 Hz with a signal-to-noise ratio of ∼ 10.

Coercivity enhancement in V2O3/Ni bilayers driven by nanoscale phase coexistence

We studied the temperature dependence of coercivity and magnetization of V2O3/Ni bilayers across the Structural Phase Transition in V2O3. We found a coercivity peak that coincides with the V2O3 phase transition on top of an overall increase of the coercivity with decreasing temperature. We propose that this sharp increase arises from a length scale competition between magnetic domains of Ni and phase coexistence during the V2O3 phase transition. This model is supported by micromagnetic simulations and shows that magnetic properties of ferromagnetic films are strongly affected by a proximal first order phase transition.

Electronic Structure Differences Between H2-, Fe-, Co-, and Cu-Phthalocyanine Highly Oriented Thin Films Observed Using NEXAFS Spectroscopy

Phthalocyanines, a class of macrocyclic, square planar molecules, are extensively studied as semiconductor materials for chemical sensors, dye-sensitized solar cells, and other applications. In this study, we use angular dependent near-edge x-ray absorption fine structure (NEXAFS) spectroscopy as a quantitative probe of the orientation and electronic structure of H2-, Fe-, Co-, and Cu-phthalocyanine molecular thin films. NEXAFS measurements at both the carbon and nitrogen K-edges reveal that phthalocyanine films deposited on sapphire have upright molecular orientations, while films up to 50 nm thick deposited on gold substrates contain prostrate molecules. Although great similarity is observed in the carbon and nitrogen K-edge NEXAFS spectra recorded for the films composed of prostrate molecules, the H2-phthalocyanine exhibits the cleanest angular dependence due to its purely out-of-plane π* resonances at the absorption onset. In contrast, organometallic-phthalocyanine nitrogen K-edges have a small in-plane resonance superimposed on this π* region that is due to a transition into molecular orbitals interacting with the 3dx(2)-y(2) empty state. NEXAFS spectra recorded at the metal L-edges for the prostrate films reveal dramatic variations in the angular dependence of specific resonances for the Cu-phthalocyanines compared with the Fe-, and Co-phthalocyanines. The Cu L3,2 edge exhibits a strong in-plane resonance, attributed to its b1g empty state with dx(2)-y(2) character at the Cu center. Conversely, the Fe- and Co- phthalocyanine L3,2 edges have strong out-of-plane resonances; these are attributed to transitions into not only b1g (dz(2)) but also eg states with dxz and dyz character at the metal center.

Effect of photodiode angular response on surface plasmon resonance measurements in the Kretschmann-Raether configuration.

We study the effect of photodiode angular response on the measurement of surface plasmon resonance (SPR) in metallic thin films using the Kretschmann-Raether configuration. The photodiode signal depends not only on the light intensity but also on the incidence angle. This implies that the photodiode sensitivity changes along the SPR curve. Consequently, the measured SPR spectrum is distorted, thus affecting fits and numerical analyses of SPR curves. We analyze the magnitude of this change, determine when it is significant, and develop a calibration method of the experimental setup which corrects for this type of spectral shape distortions.

The role of micro-shorts and electrode-film interface in the electrical transport of ultra-thin metallophthalocyanine capacitive devices

The transport properties of metallophthalocyanine thin films are important ingredients in many technological applications. Ohmic conductance of thin film (15 nm to 90 nm) Co-phthalocyanine (CoPc) capacitive devices has been investigated in the temperature range of 40 K to 300 K. For Pd and V electrodes, the electrode-film (E-F) interface and metallic micro-shorts contribute substantially to the conductance with decrease in CoPc layer thickness. A quantitative model which describes E-F interface, CoPc roughness, micro-shorts, and the exponential temperature and thickness dependence of conductance was developed. Parameters obtained from this model are in good quantitative agreement with independent measurements. The model predicts a 15-20 nm lower limit for capacitive device thickness, below which the conduction is mainly controlled by shorts. In this regime, small changes in mean CoPc thickness result in drastic variation in device conductance.

Microscopy image segmentation tool: Robust image data analysis

We present a software package called Microscopy Image Segmentation Tool (MIST). MIST is designed for analysis of microscopy images which contain large collections of small regions of interest (ROIs). Originally developed for analysis of porous anodic alumina scanning electron images, MIST capabilities have been expanded to allow use in a large variety of problems including analysis of biological tissue, inorganic and organic film grain structure, as well as nano- and meso-scopic structures. MIST provides a robust segmentation algorithm for the ROIs, includes many useful analysis capabilities, and is highly flexible allowing incorporation of specialized user developed analysis. We describe the unique advantages MIST has over existing analysis software. In addition, we present a number of diverse applications to scanning electron microscopy, atomic force microscopy, magnetic force microscopy, scanning tunneling microscopy, and fluorescent confocal laser scanning microscopy.

Low vibration high numerical aperture automated variable temperature Raman microscope

Raman micro-spectroscopy is well suited for studying a variety of properties and has been applied to a wide range of areas. Combined with tuneable temperature, Raman spectra can offer even more insights into the properties of materials. However, previous designs of variable temperature Raman microscopes have made it extremely challenging to measure samples with low signal levels due to thermal and positional instabilities as well as low collection efficiencies. Thus contemporary Raman microscope has found limited applicability to probing the subtle physics involved in phase transitions and hysteresis. This paper describes a new design of a closed-cycle, Raman microscope with full polarization rotation. High collection efficiency, thermal stability, and mechanical stability are ensured by both deliberate optical, cryogenic, and mechanical design. Measurements on two samples, Bi2Se3 and V2O3, which are challenging due to low thermal conductivities, low signal levels, and/or hysteretic effects, are measured with previously undemonstrated temperature resolution.

Study of Co-phthalocyanine films by surface plasmon resonance spectroscopy

We present a Surface Plasmon Resonance spectroscopy study of Co-Phthalocyanine (CoPc) thin films grown on Au layers at different substrate temperatures. We demonstrate that for quantitative analysis, fitting of the resonance angle alone is insufficient and Whole Curve Analysis (WCA) needs to be performed. This is because CoPc thin film dielectric constant and thickness are strongly affected by substrate temperature, even when the total deposited mass remains fixed. Using WCA, we are able to uniquely fit both the dielectric constants and the thicknesses of the films without making a priori assumptions.

Two state coercivity driven by phase coexistence in vanadium sesquioxide/nickel bulk hybrid material

We developed a bulk hybrid material consisting of a vanadium sesquioxide (V2O3) matrix with nickel (Ni) rich inclusions that exhibit a switchable two-state magnetic coercivity. The V2O3 matrix magnetoelastically couples with the Ni-rich inclusions and its structural phase transition causes two possible magnetic coercivity states. Differences of up to 13% in the temperature window of 14 K are observed, depending whether the transition occurs from rhombohedral to monoclinic or vice versa. These findings provide a pathway for the development of bulk switchable coercivity materials. We present routes to further enhance the magnetoelastic effect by increasing the oxide/ferromagnetic material coupling.

Nonequilibrium Phase Precursors during a Photoexcited Insulator-to-Metal Transition in V2O3

Here, we photoinduce and directly observe with x-ray scattering an ultrafast enhancement of the structural long-range order in the archetypal Mott system V_{2}O_{3}. Despite the ultrafast increase in crystal symmetry, the change of unit cell volume occurs an order of magnitude slower and coincides with the insulator-to-metal transition. The decoupling between the two structural responses in the time domain highlights the existence of a transient photoinduced precursor phase, which is distinct from the two structural phases present in equilibrium. X-ray nanoscopy reveals that acoustic phonons trapped in nanoscale twin domains govern the dynamics of the ultrafast transition into the precursor phase, while nucleation and growth of metallic domains dictate the duration of the slower transition into the metallic phase. The enhancement of the long-range order before completion of the electronic transition demonstrates the critical role the nonequilibrium structural phases play during electronic phase transitions in correlated electrons systems.