Light Sheet Microscopy and Image Analysis of Neural Development and Programmed Cell Death in C. Elegans Embryos

The positioning of neuronal cell bodies and neurites is critical for intact functioning of the nervous system. Mapping the positions of the soma and neurites in the brains of developing embryos as important central nervous system structures are being created may yield novel insight into the role of distinct cell groups in creating these structures. New developments in microscopy have made this an excellent time to study neural development in the C. elegans embryo. In the past decade, implementations of highly light efficient methods such as single plane illumination microscopy have rendered it possible to follow development of embryonic structures in 3D with excellent temporal resolution (Huisken et al., 2004) and low phototoxicity. Recent work has resulted in quantitative characterization of the outgrowth of a single neurite in the late, rapidly moving three-fold stage of the C. elegans embryo for the first time (Christensen et al., 2015). In this thesis, I first describe the construction and programming of a single plane illumination microscope (SPIM) based on a design from Hari Shroff\u27s lab (Wu et al., 2011). The microscope is developed especially for use with C. elegans embryos and permits fast image acquisition without excessive photodamage, compared to other forms of microscopy. Second, I describe the use of the SPIM microscope to image the development of a subset of sublateral neurons, the earliest known entrants to the nerve ring (Rapti et al, in preparation), into which they grow in the 1.5-fold stage. I describe an algorithm for automatically aligning developing embryos onto one another until the beginning of the rapid embryonic movements known as twitching, which begin at the start of the twofold stage. I employ my algorithm to align a group of identically imaged embryos onto one another and deduce information about the positioning of the nerve ring in an approximately uniform coordinate system. I determine that nerve rings are precisely positioned in the embryo to within about a micrometer while the cell bodies that grow into the nerve ring are positioned over a much wider distance. My work suggests that the nerve ring grows out towards the ALA neuron as an anchor, and that twitching may begin when the developing nerve ring reaches the ALA. I additionally describe observation of new phenotypes related to the cam-1 mutation, which was previously identified as a regulator of anterior-posterior placement of the nerve ring (Kennerdell et al., 2009). Third, I describe an application of the SPIM microscope for imaging the death of the tail spike cell, a complex, multi-compartment differentiated cell which dies over a period of hours during the three-fold stage, when the animal is rapidly moving in its shell, and cannot be imaged otherwise than with a rapid, light efficient microscope such as the one described here. I determined the time course and confirmed the sequence of events of wild type tail spike cell death. Additionally, I report stronger phenotypes for some known tail spike cell death genes when imaged in the embryo, suggesting that eff-1 plays a stronger role than previously known in clearance of the distal part of the tail spike cell process, and additionally that ced-5 has a strong role in clearance of the same compartment (in addition to its known role in soma clearance). In an appendix I describe work beginning on an extension of the microscope, which will hopefully see the microscope used as a tool for selectively inducing fluorescence in individual cells and following the development of those cells in time. My results demonstrate the utility of single plane illumination microscopy for study of C. elegans embryogenesis and establish fundamental facts about the variability of the C. elegans central nervous system by making direct comparisons between animals. This work contributes to our understanding of the C. elegans nervous system by establishing fundamental bounds on the range of nerve ring positioning between individuals

Space Object Detection in Video Satellite Images Using Motion Information

Compared to ground-based observation, space-based observation is an effective approach to catalog and monitor increasing space objects. In this paper, space object detection in a video satellite image with star image background is studied. A new detection algorithm using motion information is proposed, which includes not only the known satellite attitude motion information but also the unknown object motion information. The effect of satellite attitude motion on an image is analyzed quantitatively, which can be decomposed into translation and rotation. Considering the continuity of object motion and brightness change, variable thresholding based on local image properties and detection of the previous frame is used to segment a single-frame image. Then, the algorithm uses the correlation of object motion in multiframe and satellite attitude motion information to detect the object. Experimental results with a video image from the Tiantuo-2 satellite show that this algorithm provides a good way for space object detection

Multi-Sensory Interaction for Blind and Visually Impaired People

This book conveyed the visual elements of artwork to the visually impaired through various sensory elements to open a new perspective for appreciating visual artwork. In addition, the technique of expressing a color code by integrating patterns, temperatures, scents, music, and vibrations was explored, and future research topics were presented. A holistic experience using multi-sensory interaction acquired by people with visual impairment was provided to convey the meaning and contents of the work through rich multi-sensory appreciation. A method that allows people with visual impairments to engage in artwork using a variety of senses, including touch, temperature, tactile pattern, and sound, helps them to appreciate artwork at a deeper level than can be achieved with hearing or touch alone. The development of such art appreciation aids for the visually impaired will ultimately improve their cultural enjoyment and strengthen their access to culture and the arts. The development of this new concept aids ultimately expands opportunities for the non-visually impaired as well as the visually impaired to enjoy works of art and breaks down the boundaries between the disabled and the non-disabled in the field of culture and arts through continuous efforts to enhance accessibility. In addition, the developed multi-sensory expression and delivery tool can be used as an educational tool to increase product and artwork accessibility and usability through multi-modal interaction. Training the multi-sensory experiences introduced in this book may lead to more vivid visual imageries or seeing with the mind’s eye

There and back again : The neural basis of migration in the Bogong moth

The Bogong moth (Agrotis infusa) is a small, night-active Australian moth that has a remarkable lifestyle. Afterhatching from its pupa in spring, it migrates over 1000 km to the Australian Alps, where it spends the summer incool alpine caves. In the beginning of autumn, the moths emerge from the caves and fly back to their breedinggrounds, where they mate, lay eggs, and die. The following year, a new generation of moths repeats the samejourney to the mountains.Migration is a difficult and dangerous task. If the moths get lost on the way, they will not arrive at the caves in timeand will instead perish in the hot Australian summer. It is therefore crucial that they are efficient and reliablenavigators. However, the brains of these moths are tiny – only 3 mm in diameter. How can such a small braincompute the trajectory of this extraordinary migration?In this thesis, I investigated the neural basis of navigation and migration in the Bogong moth. I began by describingthe Bogong moth brain in detail (Paper I). In insects, neurons in a brain region known as the central complex processspatial information and provide the spatial context for behavioural decisions. The central complex of the Bogongmoth is well developed and can be expected to have the same function as in other insects. From previous studies,we know that brain regions that are of special importance for an animal tend to be bigger. I therefore compared thevolume of several higher processing neuropils, including the central complex, across several moth species (PaperII), including both migrants and non-migrants. I found that that the relative volumes of the central complex acrossspecies were very similar. In fact, the central complex scaled hypo-isometrically, suggesting that the neural networksin this brain region are so fundamentally important that even the smallest moths cannot afford to reduce them further.Therefore, instead of being reflected in the overall volume of the central complex, migratory behaviour may bereflected in the response properties of individual neurons in this brain region. Knowing that the Bogong moth canchoose a migratory heading based on the starry sky alone, I recorded from neurons in the central brain whilepresenting the moth with a rotating starry sky (Paper III). I found several neurons that consistently responded to thisstimulus. Some of these neurons had branches in the optic lobes, the central complex or the lateral complex, whichare all associated with visual compass processing. Thus, these neuropils provide a suitable substrate for processingcompass cues during the moths’ nocturnal migration. Finally, I investigated how a compass signal in the centralcomplex is transmitted to downstream motor centres that coordinate wing and leg movement. To this end, I built acomputational model of a proposed steering network (Paper IV). I showed that this network can theoretically steerbased on input from olfaction as well as vision, providing a putative connection between the compass system in thecentral complex and thoracic motor centres. Taken together, these results have not only shed light on the neuralbasis of migration in the Bogong moth, but also on neural processing in the insect central complex and lateralaccessory lobes in general. In the future, combining these results with insights from other insects may lead to acomplete understanding of the neural basis of migration, from the sensory inputs to the behavioural output

A planet within the debris disk around the pre-main-sequence star AU Microscopii

AU Microscopii (AU Mic) is the second closest pre main sequence star, at a distance of 9.79 parsecs and with an age of 22 million years. AU Mic possesses a relatively rare and spatially resolved3 edge-on debris disk extending from about 35 to 210 astronomical units from the star, and with clumps exhibiting non-Keplerian motion. Detection of newly formed planets around such a star is challenged by the presence of spots, plage, flares and other manifestations of magnetic activity on the star. Here we report observations of a planet transiting AU Mic. The transiting planet, AU Mic b, has an orbital period of 8.46 days, an orbital distance of 0.07 astronomical units, a radius of 0.4 Jupiter radii, and a mass of less than 0.18 Jupiter masses at 3 sigma confidence. Our observations of a planet co-existing with a debris disk offer the opportunity to test the predictions of current models of planet formation and evolution.Comment: Nature, published June 24th [author spelling name fix

Autonomous Orientation and Geolocation via Celestial Objects

Based on a hemispherical sensor geometry, a novel celestial navigation system is developed to use celestial objects to determine the absolute location and orientation information without the aid of satellites via two different approaches. The first approach employs a hemispherical arrangement of light intensity sensors to determine the vector to the dominant light source. We present the sensing system to measure the sun vector via least squares method and achieve the application of a low-cost, small-sized solar compass. The system is shown to work well under ideal conditions but is susceptible to noise and uncertainties in some situations. The second approach uses camera instead of light sensor, enabling the detection of celestial objects in a much more accurate and flexible fashion. An elaborate camera calibration was conducted to mitigate lens distortion and explore the transformation from image pixel coordinates to stationary world coordinates. With suitable image processing strategies, the system is able to use images of the sun and moon for the purpose of obtaining azimuth and zenith angles in spite of various disturbances. Given the results measured with our sensing systems, a generalized geolocation method is presented to estimate the absolute location on the earth. The approach, inspired by the traditional manual intercept method, automates all of its steps in an iterative fashion. It derives both the geolocation estimates and the error intervals based on measurement noise levels. This method is superior to most traditional approaches in that it derives the estimates even with lower quality sensors

Matching and Segmentation for Multimedia Data

With the development of society, both industry and academia draw increasing attention to multimedia systems, which handle image/video data, audio data, and text data comprehensively and simultaneously. In this thesis, we mainly focus on multi-modality data understanding, combining the two subjects of Computer Vision (CV) and Natural Language Processing (NLP). Such a task is widely used in many real-world scenarios, including criminal search with language descriptions by the witness, robotic navigation with language instruction in the smart industry, terrorist tracking, missing person identification, and so on. However, such a multi-modality system still faces many challenges, limiting its performance and ability in real-life situations, including the domain gap between the modalities of vision and language, the request for high-quality datasets, and so on. Therefore, to better analyze and handle these challenges, this thesis focuses on the two fundamental tasks, including matching and segmentation. Image-Text Matching (ITM) aims to retrieve the texts (images) that describe the most relevant contents for a given image (text) query. Due to the semantic gap between the linguistic and visual domains, aligning and comparing feature representations for languages and images are still challenging. To overcome this limitation, we propose a new framework for the image-text matching task, which uses an auxiliary captioning step to enhance the image feature, where the image feature is fused with the text feature of the captioning output. As the downstream application of ITM, the language-person search is one of the specific cases where language descriptions are provided to retrieve person images, which also suffers the domain gap between linguistic and visual data. To handle this problem, we propose a transformer-based language-person search matching framework with matching conducted between words and image regions for better image-text interaction. However, collecting a large amount of training data is neither cheap nor reliable using human annotations. We further study the one-shot person Re-ID (re-identification) task aiming to match people by offering one labeled reference image for each person, where previous methods request a large number of ground-truth labels. We propose progressive sample mining and representation learning to fit the limited labels for the one-shot Re-ID task better. Referring Expression Segmentation (RES) aims to localize and segment the target according to the given language expression. Existing methods jointly consider the localization and segmentation steps, which rely on the fused visual and linguistic features for both steps. We argue that the conflict between the purpose of finding the object and generating the mask limits the RES performance. To solve this problem, we propose a parallel position-kernel-segmentation pipeline to better isolate then interact with the localization and segmentation steps. In our pipeline, linguistic information will not directly contaminate the visual feature for segmentation. Specifically, the localization step localizes the target object in the image based on the referring expression, then the visual kernel obtained from the localization step guides the segmentation step. This pipeline also enables us to train RES in a weakly-supervised way, where the pixel-level segmentation labels are replaced by click annotations on center and corner points. The position head is fully-supervised trained with the click annotations as supervision, and the segmentation head is trained with weakly-supervised segmentation losses. This thesis focus on the key limitations of the multimedia system, where the experiments prove that the proposed frameworks are effective for specific tasks. The experiments are easy to reproduce with clear details, and source codes are provided for future works aiming at these tasks

The First Habitable-Zone Earth-Sized Planet From TESS. I. Validation Of The TOI-700 System

We present the discovery and validation of a three-planet system orbiting the nearby (31.1 pc) M2 dwarf star TOI-700 (TIC 150428135). TOI-700 lies in the TESS continuous viewing zone in the Southern Ecliptic Hemisphere; observations spanning 11 sectors reveal three planets with radii ranging from 1 R⊕ to 2.6 R⊕ and orbital periods ranging from 9.98 to 37.43 days. Ground-based follow-up combined with diagnostic vetting and validation tests enables us to rule out common astrophysical false-positive scenarios and validate the system of planets. The outermost planet, TOI-700 d, has a radius of 1.19 ± 0.11 R⊕ and resides within a conservative estimate of the host star\u27s habitable zone, where it receives a flux from its star that is approximately 86% of Earth\u27s insolation. In contrast to some other low-mass stars that host Earth-sized planets in their habitable zones, TOI-700 exhibits low levels of stellar activity, presenting a valuable opportunity to study potentially rocky planets over a wide range of conditions affecting atmospheric escape. While atmospheric characterization of TOI-700 d with the James Webb Space Telescope (JWST) will be challenging, the larger sub-Neptune, TOI-700 c (R = 2.63 R⊕), will be an excellent target for JWST and future space-based observatories. TESS is scheduled to once again observe the Southern Hemisphere, and it will monitor TOI-700 for an additional 11 sectors in its extended mission. These observations should allow further constraints on the known planet parameters and searches for additional planets and transit timing variations in the system