242 research outputs found
An approach for detection of glomeruli in multisite digital pathology
peer reviewedWe present a novel bioimage informatics workflow that combines Icy and
Cytomine software and their algorithms to enable large-scale analysis
of digital slides from multiple sites. In particular, we apply this
workflow on renal biopsies and evaluate empirically our approach for
the automatic detection of glomeruli in hundreds of tissue sections
Détection automatique de glomérules en pathologie digitale
Dans cet article, nous proposons une méthodologie de détection de glomérules au sein d’images de biopsies rénales. Elle combine des techniques de traitement d’images et d’apprentissage supervisé. Nous évaluons l’approche sur des images présentant plusieurs sources de variations et montrons que les comptages automatiques sont très bien corrélés avec les comptages des expert
Learning to segment clustered amoeboid cells from brightfield microscopy via multi-task learning with adaptive weight selection
Detecting and segmenting individual cells from microscopy images is critical
to various life science applications. Traditional cell segmentation tools are
often ill-suited for applications in brightfield microscopy due to poor
contrast and intensity heterogeneity, and only a small subset are applicable to
segment cells in a cluster. In this regard, we introduce a novel supervised
technique for cell segmentation in a multi-task learning paradigm. A
combination of a multi-task loss, based on the region and cell boundary
detection, is employed for an improved prediction efficiency of the network.
The learning problem is posed in a novel min-max framework which enables
adaptive estimation of the hyper-parameters in an automatic fashion. The region
and cell boundary predictions are combined via morphological operations and
active contour model to segment individual cells.
The proposed methodology is particularly suited to segment touching cells
from brightfield microscopy images without manual interventions.
Quantitatively, we observe an overall Dice score of 0.93 on the validation set,
which is an improvement of over 15.9% on a recent unsupervised method, and
outperforms the popular supervised U-net algorithm by at least on
average
Fluid dynamics during bleb formation in migrating cells in vivo
Blebs are cellular protrusions observed in migrating cells and in cells undergoing spreading, cytokinesis, and apoptosis. Here we investigate the flow of cytoplasm during bleb formation and the concurrent changes in cell volume using zebrafish primordial germ cells (PGCs) as an in vivo model. We show that bleb inflation occurs concomitantly with cytoplasmic inflow into it and that during this process the total cell volume does not change. We thus show that bleb formation in primordial germ cells results primarily from redistribution of material within the cell rather than being driven by flow of water from an external source
Featureadapted fast slant stack
ABSTRACT (N log(N ) ), where N = n 2 is the number of pixels. This new method leads to an efficient implementation of both Feature-adapted Radon and Beamlet transforms, that outperforms our previous work
Compressed Sensing with off-axis frequency-shifting holography
This work reveals an experimental microscopy acquisition scheme successfully
combining Compressed Sensing (CS) and digital holography in off-axis and
frequency-shifting conditions. CS is a recent data acquisition theory involving
signal reconstruction from randomly undersampled measurements, exploiting the
fact that most images present some compact structure and redundancy. We propose
a genuine CS-based imaging scheme for sparse gradient images, acquiring a
diffraction map of the optical field with holographic microscopy and recovering
the signal from as little as 7% of random measurements. We report experimental
results demonstrating how CS can lead to an elegant and effective way to
reconstruct images, opening the door for new microscopy applications.Comment: vol 35, pp 871-87
Telomere tethering at the nuclear periphery is essential for efficient DNA double strand break repair in subtelomeric region
In the yeast Saccharomyces cerevisiae that lacks lamins, the nuclear pore complex (NPC) has been proposed to serve a role in chromatin organization. Here, using fluorescence microscopy in living cells, we show that nuclear pore proteins of the Nup84 core complex, Nup84p, Nup145Cp, Nup120p, and Nup133p, serve to anchor telomere XI-L at the nuclear periphery. The integrity of this complex is shown to be required for repression of a URA3 gene inserted in the subtelomeric region of this chromosome end. Furthermore, altering the integrity of this complex decreases the efficiency of repair of a DNA double-strand break (DSB) only when it is generated in the subtelomeric region, even though the repair machinery is functional. These effects are specific to the Nup84 complex. Our observations thus confirm and extend the role played by the NPC, through the Nup84 complex, in the functional organization of chromatin. They also indicate that anchoring of telomeres is essential for efficient repair of DSBs occurring therein and is important for preserving genome integrity
Cerebral microcirculation shear stress levels determine Neisseria meningitidis attachment sites along the blood–brain barrier
Neisseria meningitidis is a commensal bacterium of the human nasopharynx. Occasionally, this bacterium reaches the bloodstream and causes meningitis after crossing the blood–brain barrier by an unknown mechanism. An immunohistological study of a meningococcal sepsis case revealed that neisserial adhesion was restricted to capillaries located in low blood flow regions in the infected organs. This study led to the hypothesis that drag forces encountered by the meningococcus in the bloodstream determine its attachment site in vessels. We therefore investigated the ability of N. meningitidis to bind to endothelial cells in the presence of liquid flow mimicking the bloodstream with a laminar flow chamber. Strikingly, average blood flows reported for various organs strongly inhibited initial adhesion. As cerebral microcirculation is known to be highly heterogeneous, cerebral blood velocity was investigated at the level of individual vessels using intravital imaging of rat brain. In agreement with the histological study, shear stress levels compatible with meningococcal adhesion were only observed in capillaries, which exhibited transient reductions in flow. The flow chamber assay revealed that, after initial attachment, bacteria resisted high blood velocities and even multiplied, forming microcolonies resembling those observed in the septicemia case. These results argue that the combined mechanical properties of neisserial adhesion and blood microcirculation target meningococci to transiently underperfused cerebral capillaries and thus determine disease development
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