Posterior region seeding improved posture identification in both graphical (<i>Sides</i>) and hypergraphical (<i>Posture</i>) models while exponentially decreasing runtime.

The Sides (dashed lines) and Posture (solid lines) models are compared by Q pair presence (pre-Q: triangles, post-Q: Qs). Top 1 accuracies (red) improved across models while runtimes (blue) especially fell with T pair seeding (1 on the horizontal axis). Hypergraphical modeling especially benefited from posterior pair seeding while Sides required more context to improve.</p

Anticipating, measuring, and minimizing MEMS mirror scan error to improve laser scanning microscopy's speed and accuracy

<div><p>We describe a method to speed up <u>m</u>icro<u>e</u>lectro<u>m</u>echanical <u>s</u>ystem (MEMS) mirror scanning by > 20x, while also improving scan accuracy. We use Landweber deconvolution to determine an input voltage which would produce a desired output, based on the measured MEMS impulse response. Since the MEMS is weakly nonlinear, the observed behavior deviates from expectations, and we iteratively improve our input to minimize this deviation. This allows customizable MEMS angle vs. time with <1% deviation from the desired scan pattern. We demonstrate our technique by optimizing a point scanning microscope’s raster patterns to image mammal submandibular gland and pollen at ~10 frames/s.</p></div

Manual posture identification in two successive image volumes of Fig 1B using MIPAV.

The 20 fluorescently imaged seam cell nuclei rendered in two successive image volumes. Scale bar: 10 μm. A & B: Seam cell nuclei appearing in two successive image volumes visualized in MIPAV. The five minute interval allows the embryo to reposition between images, yielding entirely different postures. C & D: Manual seam cell identification by trained users reveals the posture. The curved lines are cubic splines as described in Fig 3C.</p

Laser scanning test rig.

<p>Test rig for characterizing mirror performance.</p

<i>Posture</i> model features include all <i>Pairs</i> features and posture-wide versions of <i>Pairs</i> features.

A) Summed ratios of pair distances. B) Summed distances between successive pair midpoints. C) Summed cosine similarities between successive left and right sides. D) Summed lateral axial twist angles. E) Summed axial twist angles. F) Summed midpoint bend angles. G) Summed planar intersection angles. (TIF)</p

Hypergraphical geometric features contextualize seam cell assignments.

Anatomically inspired geometric features describe bend and twist of a posture assignment. A: Three pairs of sequential nuclei: red, green, blue. Rectangles represent pair midpoints. The angle Θ in red is used as a degree six feature given six nuclei assignments. B, C: Degree four hypergraphical features measuring twist angles φ and τ. These angles measure posterior to anterior twist pair-to-pair and left-right twist, respectively.</p

Hypergraphical models <i>Pairs</i> and <i>Posture</i> achieved highest posture identification accuracy.

Posture identification accuracies across all N=1264 samples. Point-set matching models are listed across columns: KerGM [8] was compared to proposed EHGM models. Rows list the top x accuracy as a percentage of samples. The differences between top x accuracies across hypergraphical models highlight the difficulty in posture identification.</p

Hypergraphical models more aptly contextualized posture than a graphical model but required more computation.

Runtime (minutes) refers to the median runtime of each model in minutes. Cost ratio reports the median cost ratio, defined as the ratio of the correct posture cost to the returned posture cost. Hypergraphical models more effectively described posture than the graphical model at expense of computation.</p

The <i>Pairs</i> hypergraphical model uses expansive local contexts about each portion of the embryo.

A: The Pairs hyperedges connect local seam cell nuclei in sets of four and six. B: Degree four hyperedges connect sequential pairs of seam cells while degree six hyperedges connect sequential triplets of pairs. The posterior-most degree four hyperedge and a central degree six hyperedge are bolded.</p

Point scanning microscope test rig.

<p>Test rig for point scanning fluorescence microscopy.</p