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Nuclei instance segmentation and classification of hematoxylin and eosin (H&E) stained digital pathology images are essential for further downstream cancer diagnosis and prognosis tasks. Previous works mainly focused on bottom-up methods using a single-level feature map for segmenting nuclei instances, while multilevel feature maps seemed to be more suitable for nuclei instances with various sizes and types. In this paper, we develop an effective top-down nuclei instance segmentation and classification framework (NuHTC) based on a hybrid task cascade (HTC). The NuHTC has two new components: a watershed proposal network (WSPN) and a hybrid feature extractor (HFE). The WSPN can provide additional proposals for the region proposal network which leads the model to predict bounding boxes more precisely. The HFE at the region of interest (RoI) alignment stage can better utilize both the high-level global and the low-level semantic features. It can guide NuHTC to learn nuclei instance features with less intraclass variance. We conduct extensive experiments using our method in four public multiclass nuclei instance segmentation datasets. The quantitative results of NuHTC demonstrate its superiority in both instance segmentation and classification compared to other state-of-the-art methods.
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http://dx.doi.org/10.1016/j.media.2025.103595 | DOI Listing |
Cell Rep
September 2025
Department of Neurology, University of California, Los Angeles, David Geffen School of Medicine, Los Angeles, CA 90095, USA; Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Un
Neurodevelopmental disorders often impair multiple cognitive domains. For instance, a genetic epilepsy syndrome might cause seizures due to cortical hyperexcitability and present with memory impairments arising from hippocampal dysfunction. This study examines how a single disorder differentially affects distinct brain regions using induced pluripotent stem cell (iPSC)-derived cortical- and hippocampal-ganglionic eminence assembloids to model developmental and epileptic encephalopathy 13, a condition arising from gain-of-function mutations in the SCN8A gene encoding the sodium channel Nav1.
View Article and Find Full Text PDFJ Comp Neurol
September 2025
Center for Complex Systems and Brain Sciences, Florida Atlantic University, Boca Raton, Florida, USA.
The dorsal midline thalamus (DMT) is composed of the paraventricular (PV) and paratenial (PT) nuclei. While the anatomical and functional properties of PV are well-established, PT has remarkably received very little attention-even though the efferent projections of PV and PT are very similar. Using a combination of retrograde tracing and immunohistochemistry, we examined the anatomical inputs to PT and compared them with those to the anterior and posterior PV and to the anterodorsal nucleus of the thalamus.
View Article and Find Full Text PDFSci Rep
August 2025
Angiogenesis Group, Center for Biomedical Research of La Rioja (CIBIR), 26006, Logroño, Spain.
Cripto-1 (CR1) is an oncofetal protein involved in EGF/TGFβ signal transduction, with important functions in development, stem cell biology and cancer. Its homolog, Cripto-3 (CR3), is almost identical, with the exception of six (out of 188) amino acids. Thus, until recently, no antibody could distinguish them.
View Article and Find Full Text PDFMethods Mol Biol
August 2025
Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London, UK.
Although the outer membrane of the nuclear envelope is continuous with the endoplasmic reticulum, temporally regulated and functionally significant differences in membrane lipid composition may exist between the two nuclear membranes and between the outer nuclear membrane and the endoplasmic reticulum. Biochemical approaches to probing lipid composition are challenged when lipid dynamics must be analyzed with fine spatiotemporal resolution, for instance, within the cell cycle of a single cell. Here we describe a method to probe the distribution of phosphatidic acid and diacylglycerol, two interconvertible biosynthetic precursors for other membrane glycerophospholipids, in living cells of the model fission yeast Schizosaccharomyces pombe.
View Article and Find Full Text PDFComput Biol Med
September 2025
School of Electrical Engineering, Korea University, Seoul 02841, Republic of Korea. Electronic address:
Nuclei instance segmentation is an essential task in pathology image analysis, serving as the foundation for many downstream applications. The release of several public datasets has significantly advanced research in this area, yet many existing methods struggle with data imbalance issues. To address this challenge, this study introduces a data augmentation method, called as NucleiMix, that is designed to balance the distribution of nuclei types by increasing the number of rare-type nuclei within datasets.
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