9 research outputs found
Placental Flattening via Volumetric Parameterization
We present a volumetric mesh-based algorithm for flattening the placenta to a
canonical template to enable effective visualization of local anatomy and
function. Monitoring placental function in vivo promises to support pregnancy
assessment and to improve care outcomes. We aim to alleviate visualization and
interpretation challenges presented by the shape of the placenta when it is
attached to the curved uterine wall. To do so, we flatten the volumetric mesh
that captures placental shape to resemble the well-studied ex vivo shape. We
formulate our method as a map from the in vivo shape to a flattened template
that minimizes the symmetric Dirichlet energy to control distortion throughout
the volume. Local injectivity is enforced via constrained line search during
gradient descent. We evaluate the proposed method on 28 placenta shapes
extracted from MRI images in a clinical study of placental function. We achieve
sub-voxel accuracy in mapping the boundary of the placenta to the template
while successfully controlling distortion throughout the volume. We illustrate
how the resulting mapping of the placenta enhances visualization of placental
anatomy and function. Our code is freely available at
https://github.com/mabulnaga/placenta-flattening .Comment: MICCAI 201
AnyStar: Domain randomized universal star-convex 3D instance segmentation
Star-convex shapes arise across bio-microscopy and radiology in the form of
nuclei, nodules, metastases, and other units. Existing instance segmentation
networks for such structures train on densely labeled instances for each
dataset, which requires substantial and often impractical manual annotation
effort. Further, significant reengineering or finetuning is needed when
presented with new datasets and imaging modalities due to changes in contrast,
shape, orientation, resolution, and density. We present AnyStar, a
domain-randomized generative model that simulates synthetic training data of
blob-like objects with randomized appearance, environments, and imaging physics
to train general-purpose star-convex instance segmentation networks. As a
result, networks trained using our generative model do not require annotated
images from unseen datasets. A single network trained on our synthesized data
accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence
microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM,
and placental cotyledons in human fetal MRI, all without any retraining,
finetuning, transfer learning, or domain adaptation. Code is available at
https://github.com/neel-dey/AnyStar.Comment: Code available at https://github.com/neel-dey/AnySta
Dynamic Neural Fields for Learning Atlases of 4D Fetal MRI Time-series
We present a method for fast biomedical image atlas construction using neural
fields. Atlases are key to biomedical image analysis tasks, yet conventional
and deep network estimation methods remain time-intensive. In this preliminary
work, we frame subject-specific atlas building as learning a neural field of
deformable spatiotemporal observations. We apply our method to learning
subject-specific atlases and motion stabilization of dynamic BOLD MRI
time-series of fetuses in utero. Our method yields high-quality atlases of
fetal BOLD time-series with 5-7 faster convergence compared to
existing work. While our method slightly underperforms well-tuned baselines in
terms of anatomical overlap, it estimates templates significantly faster, thus
enabling rapid processing and stabilization of large databases of 4D dynamic
MRI acquisitions. Code is available at
https://github.com/Kidrauh/neural-atlasingComment: 6 pages, 2 figures. Accepted by Medical Imaging Meets NeurIPS 202
Volumetric Parameterization of the Placenta to a Flattened Template
We present a volumetric mesh-based algorithm for parameterizing the placenta
to a flattened template to enable effective visualization of local anatomy and
function. MRI shows potential as a research tool as it provides signals
directly related to placental function. However, due to the curved and highly
variable in vivo shape of the placenta, interpreting and visualizing these
images is difficult. We address interpretation challenges by mapping the
placenta so that it resembles the familiar ex vivo shape. We formulate the
parameterization as an optimization problem for mapping the placental shape
represented by a volumetric mesh to a flattened template. We employ the
symmetric Dirichlet energy to control local distortion throughout the volume.
Local injectivity in the mapping is enforced by a constrained line search
during the gradient descent optimization. We validate our method using a
research study of 111 placental shapes extracted from BOLD MRI images. Our
mapping achieves sub-voxel accuracy in matching the template while maintaining
low distortion throughout the volume. We demonstrate how the resulting
flattening of the placenta improves visualization of anatomy and function. Our
code is freely available at https://github.com/mabulnaga/placenta-flattening
A Toolbox to Visually Explore Cerebellar Shape Changes in Cerebellar Disease and Dysfunction
The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects’ cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature
Placental MRI: Effect of maternal position and uterine contractions on placental BOLD MRI measurements
© 2020 Elsevier Ltd Introduction: Before using blood-oxygen-level-dependent magnetic resonance imaging (BOLD MRI) during maternal hyperoxia as a method to detect individual placental dysfunction, it is necessary to understand spatiotemporal variations that represent normal placental function. We investigated the effect of maternal position and Braxton-Hicks contractions on estimates obtained from BOLD MRI of the placenta during maternal hyperoxia. Methods: For 24 uncomplicated singleton pregnancies (gestational age 27–36 weeks), two separate BOLD MRI datasets were acquired, one in the supine and one in the left lateral maternal position. The maternal oxygenation was adjusted as 5 min of room air (21% O2), followed by 5 min of 100% FiO2. After datasets were corrected for signal non-uniformities and motion, global and regional BOLD signal changes in R2* and voxel-wise Time-To-Plateau (TTP) in the placenta were measured. The overall placental and uterine volume changes were determined across time to detect contractions. Results: In mothers without contractions, increases in global placental R2* in the supine position were larger compared to the left lateral position with maternal hyperoxia. Maternal position did not alter global TTP but did result in regional changes in TTP. 57% of the subjects had Braxton-Hicks contractions and 58% of these had global placental R2* decreases during the contraction. Conclusion: Both maternal position and Braxton-Hicks contractions significantly affect global and regional changes in placental R2* and regional TTP. This suggests that both factors must be taken into account in analyses when comparing placental BOLD signals over time within and between individuals