Enhancement of Underwater Video Mosaics for Post-Processing

Mosaics of seafloor created from still images or video acquired underwater have proved to be useful for construction of maps of forensic and archeological sites, species\u27 abundance estimates, habitat characterization, etc. Images taken by a camera mounted on a stable platform are registered (at first pair-wise and then globally) and assembled in a high resolution visual map of the surveyed area. While this map is usually sufficient for a human orientation and even quantitative measurements, it often contains artifacts that complicate an automatic post-processing (for example, extraction of shapes for organism counting, or segmentation for habitat characterization). The most prominent artifacts are inter-frame seams caused by inhomogeneous artificial illumination, and local feature misalignments due to parallax effects - result of an attempt to represent a 3D world on a 2D map. In this paper we propose two image processing techniques for mosaic quality enhancement - median mosaic-based illumination correction suppressing appearance of inter-frame seams, and micro warping decreasing influence of parallax effects

Overcoming the Challenges Associated with Image-based Mapping of Small Bodies in Preparation for the OSIRIS-REx Mission to (101955) Bennu

The OSIRIS-REx Asteroid Sample Return Mission is the third mission in NASA's New Frontiers Program and is the first U.S. mission to return samples from an asteroid to Earth. The most important decision ahead of the OSIRIS-REx team is the selection of a prime sample-site on the surface of asteroid (101955) Bennu. Mission success hinges on identifying a site that is safe and has regolith that can readily be ingested by the spacecraft's sampling mechanism. To inform this mission-critical decision, the surface of Bennu is mapped using the OSIRIS-REx Camera Suite and the images are used to develop several foundational data products. Acquiring the necessary inputs to these data products requires observational strategies that are defined specifically to overcome the challenges associated with mapping a small irregular body. We present these strategies in the context of assessing candidate sample-sites at Bennu according to a framework of decisions regarding the relative safety, sampleability, and scientific value across the asteroid's surface. To create data products that aid these assessments, we describe the best practices developed by the OSIRIS-REx team for image-based mapping of irregular small bodies. We emphasize the importance of using 3D shape models and the ability to work in body-fixed rectangular coordinates when dealing with planetary surfaces that cannot be uniquely addressed by body-fixed latitude and longitude.Comment: 31 pages, 10 figures, 2 table

Image Sampling with Quasicrystals

We investigate the use of quasicrystals in image sampling. Quasicrystals produce space-filling, non-periodic point sets that are uniformly discrete and relatively dense, thereby ensuring the sample sites are evenly spread out throughout the sampled image. Their self-similar structure can be attractive for creating sampling patterns endowed with a decorative symmetry. We present a brief general overview of the algebraic theory of cut-and-project quasicrystals based on the geometry of the golden ratio. To assess the practical utility of quasicrystal sampling, we evaluate the visual effects of a variety of non-adaptive image sampling strategies on photorealistic image reconstruction and non-photorealistic image rendering used in multiresolution image representations. For computer visualization of point sets used in image sampling, we introduce a mosaic rendering technique.Comment: For a full resolution version of this paper, along with supplementary materials, please visit at http://www.Eyemaginary.com/Portfolio/Publications.htm

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

Motivation: Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

Motivation: Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections

As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets

Motivation: Tiled serial section Transmission Electron Microscopy (ssTEM) is increasingly used to describe high-resolution anatomy of large biological specimens. In particular in neurobiology, TEM is indispensable for analysis of synaptic connectivity in the brain. Registration of ssTEM image mosaics has to recover the 3D continuity and geometrical properties of the specimen in presence of various distortions that are applied to the tissue during sectioning, staining and imaging. These include staining artifacts, mechanical deformation, missing sections and the fact that structures may appear dissimilar in consecutive sections. Results: We developed a fully automatic, non-rigid but as-rigid-as-possible registration method for large tiled serial section microscopy stacks. We use the Scale Invariant Feature Transform (SIFT) to identify corresponding landmarks within and across sections and globally optimize the pose of all tiles in terms of least square displacement of these landmark correspondences. We evaluate the precision of the approach using an artificially generated dataset designed to mimic the properties of TEM data. We demonstrate the performance of our method by registering an ssTEM dataset of the first instar larval brain of Drosophila melanogaster consisting of 6885 images. Availability: This method is implemented as part of the open source software TrakEM2 (http://www.ini.uzh.ch/∼acardona/trakem2.html) and distributed through the Fiji project (http://pacific.mpi-cbg.de). Contact: [email protected]

Globally optimal stitching of tiled 3D microscopic image acquisitions

Motivation: Modern anatomical and developmental studies often require high-resolution imaging of large specimens in three dimensions (3D). Confocal microscopy produces high-resolution 3D images, but is limited by a relatively small field of view compared with the size of large biological specimens. Therefore, motorized stages that move the sample are used to create a tiled scan of the whole specimen. The physical coordinates provided by the microscope stage are not precise enough to allow direct reconstruction (Stitching) of the whole image from individual image stacks