31,689 research outputs found
Promising Deep Semantic Nuclei Segmentation Models for Multi-Institutional Histopathology Images of Different Organs
Nuclei segmentation in whole-slide imaging (WSI) plays a crucial role in the field of computational pathology. It is a fundamental task for different applications, such as cancer cell type classification, cancer grading, and cancer subtype classification. However, existing nuclei segmentation methods face many challenges, such as color variation in histopathological images, the overlapping and clumped nuclei, and the ambiguous boundary between different cell nuclei, that limit their performance. In this paper, we present promising deep semantic nuclei segmentation models for multi-institutional WSI images (i.e., collected from different scanners) of different organs. Specifically, we study the performance of pertinent deep learning-based models with nuclei segmentation in WSI images of different stains and various organs. We also propose a feasible deep learning nuclei segmentation model formed by combining robust deep learning architectures. A comprehensive comparative study with existing software and related methods in terms of different evaluation metrics and the number of parameters of each model, emphasizes the efficacy of the proposed nuclei segmentation models
Diffusion-based Data Augmentation for Nuclei Image Segmentation
Nuclei segmentation is a fundamental but challenging task in the quantitative
analysis of histopathology images. Although fully-supervised deep
learning-based methods have made significant progress, a large number of
labeled images are required to achieve great segmentation performance.
Considering that manually labeling all nuclei instances for a dataset is
inefficient, obtaining a large-scale human-annotated dataset is time-consuming
and labor-intensive. Therefore, augmenting a dataset with only a few labeled
images to improve the segmentation performance is of significant research and
application value. In this paper, we introduce the first diffusion-based
augmentation method for nuclei segmentation. The idea is to synthesize a large
number of labeled images to facilitate training the segmentation model. To
achieve this, we propose a two-step strategy. In the first step, we train an
unconditional diffusion model to synthesize the Nuclei Structure that is
defined as the representation of pixel-level semantic and distance transform.
Each synthetic nuclei structure will serve as a constraint on histopathology
image synthesis and is further post-processed to be an instance map. In the
second step, we train a conditioned diffusion model to synthesize
histopathology images based on nuclei structures. The synthetic histopathology
images paired with synthetic instance maps will be added to the real dataset
for training the segmentation model. The experimental results show that by
augmenting 10% labeled real dataset with synthetic samples, one can achieve
comparable segmentation results with the fully-supervised baseline.Comment: MICCAI 2023, released code: https://github.com/lhaof/Nudif
Region-Based PDEs for Cells Counting and Segmentation in 3D+Time Images of Vertebrate Early Embryogenesis
This paper is devoted to the segmentation of cell nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. The segmentation allows to identify and quantify the number of cells in the animal model. This kind of information is relevant to estimate important biological parameters such as the cell proliferation rate in time and space. Our approach is based on the active contour model without edges. We compare two different formulations of the model equation and evaluate their performances in segmenting nuclei of different shapes and sizes. Qualitative and quantitative comparisons are performed on both synthetic and real data, by means of suitable gold standard. The best approach is then applied on a number of time lapses for the segmentation and counting of cells during the development of a zebrafish embryo between the sphere and the shield stage
MGTUNet: An new UNet for colon nuclei instance segmentation and quantification
Colorectal cancer (CRC) is among the top three malignant tumor types in terms
of morbidity and mortality. Histopathological images are the gold standard for
diagnosing colon cancer. Cellular nuclei instance segmentation and
classification, and nuclear component regression tasks can aid in the analysis
of the tumor microenvironment in colon tissue. Traditional methods are still
unable to handle both types of tasks end-to-end at the same time, and have poor
prediction accuracy and high application costs. This paper proposes a new UNet
model for handling nuclei based on the UNet framework, called MGTUNet, which
uses Mish, Group normalization and transposed convolution layer to improve the
segmentation model, and a ranger optimizer to adjust the SmoothL1Loss values.
Secondly, it uses different channels to segment and classify different types of
nucleus, ultimately completing the nuclei instance segmentation and
classification task, and the nuclei component regression task simultaneously.
Finally, we did extensive comparison experiments using eight segmentation
models. By comparing the three evaluation metrics and the parameter sizes of
the models, MGTUNet obtained 0.6254 on PQ, 0.6359 on mPQ, and 0.8695 on R2.
Thus, the experiments demonstrated that MGTUNet is now a state-of-the-art
method for quantifying histopathological images of colon cancer.Comment: Published in BIBM2022(regular
paper),https://doi.org/10.1109/BIBM55620.2022.999566
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