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Biologically Inspired Robotics and Dynamical Systems (BIRDS) Lab
User Collection- Creator:
- Revzen, Shai
- Description:
- Professor Revzen and his team at the Biologically Inspired Robotics and Dynamical Systems (BIRDS) Lab are working on discovering, modeling, and reproducing the strategies animals use when interacting with physical objects. This work consists of collaboration with biomechanists to analyze experimental data, developing new mathematical tools for modeling and estimation of model parameters, and construction of robots which employ the new principles.
- Discipline:
- Science
7Works -
- Creator:
- Figueroa, Carlos A., Computational Vascular Biomechanics Lab, University of Michigan, and et al.
- Description:
- This collection concerns the CRIMSON (CardiovasculaR Integrated Modelling and SimulatiON) software environment. CRIMSON provides a powerful, customizable and user-friendly system for performing three-dimensional and reduced-order computational haemodynamics studies via a pipeline which involves: 1) segmenting vascular structures from medical images; 2) constructing analytic arterial and venous geometric models; 3) performing finite element mesh generation; 4) designing, and 5) applying boundary conditions; 6) running incompressible Navier-Stokes simulations of blood flow with fluid-structure interaction capabilities; and 7) post-processing and visualizing the results, including velocity, pressure and wall shear stress fields. , The minimum specifications to run CRIMSON are: Any AMD64 CPU (note: Intel Core i series are AMD64), Windows (only tested on Windows 10 but might work on Windows 7), 8 GB of RAM , If you are running non-trivial models you will want to have: Quad core CPU or higher, Solid state drive for storing data, Windows, 16 GB of RAM, Dedicated discrete GPU for rendering models. , and Software in this collection is a snapshot; please visit https://github.com/carthurs/CRIMSONGUI & www.crimson.software for more general information and the most up to date version of the software.
- Keyword:
- Blood Flow Simulation, Patient-specific, Open-source Software, Image-based simulation, Cardiovascular Medical Image, Segmentation, and Finite Element Simulation
- Citation to related publication:
- CRIMSON: An Open-Source Software Framework for Cardiovascular Integrated Modelling and Simulation C.J. Arthurs, R. Khlebnikov, A. Melville, et al. bioRxiv 2020.10.14.339960; doi: https://doi.org/10.1101/2020.10.14.339960
- Discipline:
- Health Sciences and Engineering
4Works -
Lu-177 DOTATATE Anonymized Patient Datasets
User Collection- Creator:
- Dewaraja, Yuni K and Van, Benjamin J
- Description:
- This collection is comprised of a number of works that collectively represent the imaging studies and information necessary for dosimetric analysis of a patient treated with Lutathera. All works may be used as standalone datasets or in conjunction with the others in this collection depending on the analysis performed. Files are stored using the DICOM standard widely accepted for storage and transmission of medical images and related information. All patient private information has been anonymized using MIM commercial software (MIM Software Inc.). Data from 2 patients, referred to as patient 4 and patient 6, has been provided in this collection and is divided among 6 works as outlined below:, 1) Pre-Therapy Diagnostic Images. Description: Patient diagnostic scans performed prior to Lutathera treatment. Used for identifying lesions and measuring progression. Note that the date of the baseline scan may be several months before the Lutathera treatment and changes in the anatomy are possible. Files: (1) Ga68 Dotatate PET/CT, Either: (1) MRI, (1) standalone diagnostic CT, 2) Planar Whole Body Scans. Description: Planar whole body Lu-177 scans taken at 4 time points within a week after treatment. Two views (Anterior and Posterior) and 3 energy windows (one main window at 208 keV and 2 adjacent scatter windows) are available for each time point. The units of this image is counts. Energy window information, acquisition data/time and duration can be found in DICOM header. Files: (6) individual images at each time point (24 total images per patient) , 3) SPECT/CT Scans. Description: Lu-177 SPECT/CT scans at 4 time points within a week after treatment (same time points as the planar scans). Images were acquired on a Siemens Intevo system and reconstructed using xSPECT Quant. The units of this image is Bq/mL. Information on the reconstruction, acquisition date/time, duration, Lu-177 administration time and activity can be found in the DICOM header. Files: (1) Folder with reconstructed SPECT slices per time point (4 folders total per patient), (1) Folder containing co-registered CT slices per time point (4 folders total per patient), 4) Lesion and Organ Volumes of Interest. Description: DICOM RT structure files containing organ and lesion volumes of interest (VOI) that were defined on the CT of the scan1 SPECT/CT in 3). Organs were defined using semi-automatic tools (atlas based and CNN-based) while lesions were defined manually by a radiologist guided by baseline scans. Only lesions >2 cc were defined. Files: (1) File containing organ contours, (1) File containing lesion contours, 5) Time Integrated Activity Maps. Description: A DICOM file containing the time-integrated activity map over all 4 time points within a week after treatment. This combines the SPECT/CT scans provided in 3) into a single integrated activity map. This map was generated via the MIM MRT Dosimetry package: The 4 time points were registered to the reference SPECT scan (time point 1) using a contour intensity based SPECT alignment and the voxel-level time-activity data was fit using exponential functions. Voxel-level integration was performed to generate the TIA map. The units of this image is Bq/mL * sec. Files: (1) Folder with Time-integrated activity image per patient, and 6) Projection Data and CT based Attenuation Coefficient Maps. Description: SPECT projection data for each of the 4 Lutathera scans taken within a week after treatment is provided in 3 forms: unaltered, Siemens [Reformatted], and Siemens [Advanced]. The difference between the Projections and the [Advanced] Projections is that the [Advanced] consists of uncorrected raw projection data and the other the corrected projection data (e.g. camera uniformity corrections). The [Advanced] projections are used in xSPECT reconstruction (where all corrections are done during the reconstruction), while the other is used in Flash 3D reconstruction. CT-based attenuation coefficient maps (mumaps) are provided for each of the 4 scans taken within a week after treatment. Two methods are provided for each mumap: xSPECT and F3D as the matrix size is different for the 2 cases (256 x 256 for xSPECT and 128 x 128 for Flash3D). Files: (3) Folders containing raw SPECT projections, (2) Folders containing CT attenuation coefficient maps (mumaps)
- Keyword:
- Lu-177, Lutathera, Dosimetry, Radionuclide, and CTMRIPET
- Discipline:
- Health Sciences
6Works -
Division of Fishes
User Collection- Creator:
- University of Michigan Museum of Zoology
- Description:
- Division of Fishes
- Discipline:
- Science
48Works -
Defect patterns on the curved surface of fish retinae suggest a mechanism of cone mosaic formation
User Collection- Creator:
- Nunley, Hayden, Nagashima, Mikiko, Martin, Kamirah, Lorenzo Gonzalez, Alcides, Suzuki, Sachihiro C., Norton, Declan A., Wong, Rachel O. L., Raymond, Pamela A., and Lubensky, David K.
- Description:
- The outer epithelial layer of zebrafish retinae contains a crystalline array of cone photoreceptors, called the cone mosaic. As this mosaic grows by mitotic addition of new photoreceptors at the rim of the hemispheric retina, topological defects, called “Y-Junctions”, form to maintain approximately constant cell spacing. The generation of topological defects due to growth on a curved surface is a distinct feature of the cone mosaic not seen in other well-studied biological patterns like the R8 photoreceptor array in the _ Drosophila compound eye. Since defects can provide insight into cell-cell interactions responsible for pattern formation, here we characterize the arrangement of cones in individual Y-Junction cores (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7) as well as the spatial distribution of Y-junctions across entire retinae (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae). We find that for individual Y-junctions, the distribution of cones near the core corresponds closely to structures observed in physical crystals (see Set of images for Figures 1 and 2 and 6 and Supplementary Figure 7). In addition, Y-Junctions are organized into lines, called grain boundaries, from the retinal center to the periphery (see Dataset for analyzing spatial distribution of Y-junctions in flat-mounted retinae and Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae). In physical crystals, regardless of the initial distribution of defects, defects can coalesce into grain boundaries via the mobility of individual particles. By imaging in live fish, we demonstrate that grain boundaries in the cone mosaic instead appear during initial mosaic formation, without requiring defect motion (see Dataset for measuring tendency of Y-junctions to line up into grain boundaries during incorporation into retinae and Dataset for analyzing Y-junction motion in live fish retinae). Motivated by this observation, we show that a computational model of repulsive cell-cell interactions generates a mosaic with grain boundaries (see Code and example simulations of phase-field crystal model (for cone mosaic formation)). In contrast to paradigmatic models of fate specification in mostly motionless cell packings (see Code and accompanying input data for simulating lateral inhibition on motionless cell packing), this finding emphasizes the role of cell motion, guided by cell-cell interactions during differentiation, in forming biological crystals. Such a route to the formation of regular patterns may be especially valuable in situations, like growth on a curved surface, where the resulting long-ranged, elastic, effective interactions between defects can help to group them into grain boundaries.
- Keyword:
- zebrafish cone mosaic, lattice vectors, topological defects, tissue patterning, grain boundaries, lateral inhibition, photoconversion, phase-field crystal model, and defect motion
- Discipline:
- Science
7Works -
- Creator:
- Huang, Cheng MI
- Description:
- This collection contains a hierarchy of test problems for turbulent reacting flow simulations. It is meant to provide a testbed to build reduced model for relevant challenging reacting flow problems using different methods. In addition, this collection also serves to engage a broad community of experts in computational science and the field of engineering to address certain challenges in constructing reduced models for reacting flow simulations. All the datasets in this collection were generated under the Air Force Center of Excellence on Multi-Fidelity Modeling of Rocket Combustion Dynamics and the goal of the center is to advance the state-of-the-art in Reduced Order Models (ROMs) and enable efficient and accurate prediction of instabilities in liquid fueled rocket combustion systems.
- Discipline:
- Engineering
2Works -
Vani Region Archaeological Survey
User Collection- Creator:
- Ratte, Christopher and Mokrisova, Jana
- Description:
- The data presented here were collected in the course of an archaeological survey of the region around Vani in the Republic of Georgia, carried out between 2009 and 2011, with follow-up visits in 2014 and 2017. The survey was sponsored by the University of Michigan, the Institute for the Study of the Ancient World at New York University, and the Otar Lordkipanidze Institute of Archaeological Research in Tbilisi. , The archaeological site of Vani lies in the territory of ancient Colchis, a triangular area bordered by the Black Sea to the west and by the greater and lesser Caucasus Mountains to the north and south – famous in Greek legend as the land of the Golden Fleece and the home of Medea. Vani itself is situated approximately 70 km inland, in the foothills of the lesser Caucasus. A regional culture recognizable on the evidence of distinctive traditions of pottery and metalworking and the appearance of a network of relatively large settlements had emerged in Colchis by the late second and early first millennia BC. , Vani is one of the most extensively studied archaeological sites in Colchis. Excavations have revealed a continuous occupation sequence extending from the 8th to the 1st centuries B.C. Especially notable are the rich and unusual graves of the Classical period (6th-4th centuries), the monumental stone architecture of the Hellenistic period (3rd to 1st centuries), especially fortifications enclosing an area of approximately 6 ha, and the extensive evidence for interaction with the Mediterranean and Near Eastern worlds, including not only commercial and luxury imports (Greek transport amphorae, fine bronze and silver utensils from both the Greek world and Persia), but also local production of bronze sculpture and one long Greek bronze inscription., In spite of the richness of the site, however, important questions about its purpose and function over time remain unresolved. How extensive was the ancient settlement? Was Vani an isolated stronghold, a regional population center, a sanctuary, or a combination of two or all three? How does it compare with other sites in Colchis? In addition to ongoing research at Vani itself, regional survey provides an obvious approach to some of these questions. In previous years, examination of a number of outlying sites had already yielded remains extending in date from the Early Bronze Age to the mediaeval period., and The purpose of the regional survey project begun in 2009 was to integrate existing knowledge about Vani and environs into the kind of technological and conceptual framework characteristic of contemporary American survey archaeology. Of particular importance was the use of Geographical Information Systems (GIS) as an organizational and analytical tool, and of geophysical prospection both in the immediate environs of Vani and at regional sites. Like all regional surveys, our project recorded evidence of all periods, from prehistory to the present day, but we were particularly interested in questions having to do with the increasing social complexity of Colchis in the mid- and later 1st millennium BC – when Greek explorers began to establish colonies on the Black Sea coast of Georgia, and the Persian empire pushed up against the mountains of the Caucasus. What was the nature of Colchian society in this period? How was it affected by interaction with the larger Greek, Persian, and Pontic worlds? And how can regional survey at Vani and throughout Colchis help us to address these questions?
- Keyword:
- Classical Archaeology, Fortifications, Churches, Sanctuaries, Quarries, Modern Settlements, Settlements, and Burials
- Discipline:
- Humanities
25Sub-collections1Works -
Radionuclide PET/CT, SPECT/CT, and Contours Collection
User Collection- Creator:
- Van, Benjamin and Dewaraja, Yuni
- Description:
- Interest in quantitative imaging of Y-90 and Lu-177 is growing due to their increased use as minimally invasive treatments for primary and metastatic tumors such as HCC and NETs. Accurate quantification of the 3D activity distribution for voxel-level dosimetry requires SPECT/CT and PET/CT imaging. This collection provides research access to anonymized PET/CT and SPECT/CT scans along with the relevant lesion/organ contours taken from University of Michigan clinical research studies of selected patients undergoing radionuclide treatments. All patients signed an informed consent to participate in the research studies. See the readme in each dataset for information on use and citation of this data.
- Discipline:
- Health Sciences
1Works -
S’Urachi Site-Based Archaeological Survey
User Collection- Creator:
- Gosner, Linda R.
- Description:
- This data was produced by the site-based archaeological survey at the nuraghe S'Urachi in west-central Sardinia (San Vero Milis, Oristano, Sardinia). The survey was carried out from 2015-2017 as a part of the ongoing Progetto S'Urachi, an archaeological project that aims to understand daily life around the monumental Bronze Age tower of S'Urachi during the later occupation of the landscape over the course of the 1st millennium BCE.
- Keyword:
- Mediterranean archaeology, Sardinia, Archaeological Survey, Excavation, and Classical Archaeology
- Discipline:
- Social Sciences
2Works -
Estimates of the water balance of the Laurentian Great Lakes using the Large Lakes Statistical Water Balance Model (L2SWBM)
User Collection- Creator:
- Smith, Joeseph P., Fry, Lauren M., Do, Hong X., and Gronewold, Andrew D.
- Description:
- This collection contains estimates of the water balance of the Laurentian Great Lakes that were produced by the Large Lakes Statistical Water Balance Model (L2SWBM). Each data set has a different configuration and was used as the supplementary for a published peer-reviewed article (see "Citations to related material" section in the metadata of individual data sets). The key variables that were estimated by the L2SWBM are (1) over-lake precipitation, (2) over-lake evaporation, (3) lateral runoff, (4) connecting-channel outflows, (5) diversions, and (6) predictive changes in lake storage. and Contact: Andrew Gronewold Office: 4040 Dana Phone: (734) 764-6286 Email: drewgron@umich.edu
- Keyword:
- Great Lakes water levels, statistical inference, water balance, data assimilation, Great Lakes, Laurentian, Machine learning, Bayesian, and Network
- Citation to related publication:
- Smith, J. P., & Gronewold, A. D. (2017). Development and analysis of a Bayesian water balance model for large lake systems. arXiv preprint arXiv:1710.10161., Gronewold, A. D., Smith, J. P., Read, L., & Crooks, J. L. (2020). Reconciling the water balance of large lake systems. Advances in Water Resources, 103505., and Do, H.X., Smith, J., Fry, L.M., and Gronewold, A.D., Seventy-year long record of monthly water balance estimates for Earth’s largest lake system (under revision)
- Discipline:
- Science and Engineering
5Works