A kinetic approach to consensus-based segmentation of biomedical images
- URL: http://arxiv.org/abs/2211.05226v2
- Date: Fri, 14 Jun 2024 15:52:29 GMT
- Title: A kinetic approach to consensus-based segmentation of biomedical images
- Authors: Raffaella Fiamma Cabini, Anna Pichiecchio, Alessandro Lascialfari, Silvia Figini, Mattia Zanella,
- Abstract summary: We apply a kinetic version of a bounded confidence consensus model to biomedical segmentation problems.
The large time behavior of the system is then computed with the aid of a surrogate Fokker-Planck approach.
We minimize the introduced segmentation metric for a relevant set of 2D gray-scale images.
- Score: 39.58317527488534
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: In this work, we apply a kinetic version of a bounded confidence consensus model to biomedical segmentation problems. In the presented approach, time-dependent information on the microscopic state of each particle/pixel includes its space position and a feature representing a static characteristic of the system, i.e. the gray level of each pixel. From the introduced microscopic model we derive a kinetic formulation of the model. The large time behavior of the system is then computed with the aid of a surrogate Fokker-Planck approach that can be obtained in the quasi-invariant scaling. We exploit the computational efficiency of direct simulation Monte Carlo methods for the obtained Boltzmann-type description of the problem for parameter identification tasks. Based on a suitable loss function measuring the distance between the ground truth segmentation mask and the evaluated mask, we minimize the introduced segmentation metric for a relevant set of 2D gray-scale images. Applications to biomedical segmentation concentrate on different imaging research contexts.
Related papers
- Introducing Shape Prior Module in Diffusion Model for Medical Image
Segmentation [7.7545714516743045]
We propose an end-to-end framework called VerseDiff-UNet, which leverages the denoising diffusion probabilistic model (DDPM)
Our approach integrates the diffusion model into a standard U-shaped architecture.
We evaluate our method on a single dataset of spine images acquired through X-ray imaging.
arXiv Detail & Related papers (2023-09-12T03:05:00Z) - A Segmentation Method for fluorescence images without a machine learning
approach [0.0]
This study describes a deterministic computational neuroscience approach for identifying cells and nuclei.
The method is robust, based on formally correct functions, and does not suffer from tuning on specific data sets.
arXiv Detail & Related papers (2022-12-28T16:47:05Z) - Stain-invariant self supervised learning for histopathology image
analysis [74.98663573628743]
We present a self-supervised algorithm for several classification tasks within hematoxylin and eosin stained images of breast cancer.
Our method achieves the state-of-the-art performance on several publicly available breast cancer datasets.
arXiv Detail & Related papers (2022-11-14T18:16:36Z) - Amortized Inference for Heterogeneous Reconstruction in Cryo-EM [36.911133113707045]
cryo-electron microscopy (cryo-EM) provides insights into the dynamics of proteins and other building blocks of life.
The algorithmic challenge of jointly estimating the poses, 3D structure, and conformational heterogeneity of a biomolecule remains unsolved.
Our method, cryoFIRE, performs ab initio heterogeneous reconstruction with unknown poses in an amortized framework.
We show that our method can provide one order of magnitude speedup on datasets containing millions of images without any loss of accuracy.
arXiv Detail & Related papers (2022-10-13T22:06:38Z) - Dynamic multi feature-class Gaussian process models [0.0]
This study presents a statistical modelling method for automatic learning of shape, pose and intensity features in medical images.
A DMFC-GPM is a Gaussian process (GP)-based model with a shared latent space that encodes linear and non-linear variation.
The model performance results suggest that this new modelling paradigm is robust, accurate, accessible, and has potential applications.
arXiv Detail & Related papers (2021-12-08T15:12:47Z) - Automatic size and pose homogenization with spatial transformer network
to improve and accelerate pediatric segmentation [51.916106055115755]
We propose a new CNN architecture that is pose and scale invariant thanks to the use of Spatial Transformer Network (STN)
Our architecture is composed of three sequential modules that are estimated together during training.
We test the proposed method in kidney and renal tumor segmentation on abdominal pediatric CT scanners.
arXiv Detail & Related papers (2021-07-06T14:50:03Z) - Assignment Flow for Order-Constrained OCT Segmentation [0.0]
The identification of retinal layer thicknesses serves as an essential task be done for each patient separately.
The elaboration of automated segmentation models has become an important task in the field of medical image processing.
We propose a novel, purely data driven textitgeometric approach to order-constrained 3D OCT retinal cell layer segmentation
arXiv Detail & Related papers (2020-09-10T01:57:53Z) - Improved Slice-wise Tumour Detection in Brain MRIs by Computing
Dissimilarities between Latent Representations [68.8204255655161]
Anomaly detection for Magnetic Resonance Images (MRIs) can be solved with unsupervised methods.
We have proposed a slice-wise semi-supervised method for tumour detection based on the computation of a dissimilarity function in the latent space of a Variational AutoEncoder.
We show that by training the models on higher resolution images and by improving the quality of the reconstructions, we obtain results which are comparable with different baselines.
arXiv Detail & Related papers (2020-07-24T14:02:09Z) - Unsupervised Instance Segmentation in Microscopy Images via Panoptic
Domain Adaptation and Task Re-weighting [86.33696045574692]
We propose a Cycle Consistency Panoptic Domain Adaptive Mask R-CNN (CyC-PDAM) architecture for unsupervised nuclei segmentation in histopathology images.
We first propose a nuclei inpainting mechanism to remove the auxiliary generated objects in the synthesized images.
Secondly, a semantic branch with a domain discriminator is designed to achieve panoptic-level domain adaptation.
arXiv Detail & Related papers (2020-05-05T11:08:26Z) - Pathological Retinal Region Segmentation From OCT Images Using Geometric
Relation Based Augmentation [84.7571086566595]
We propose improvements over previous GAN-based medical image synthesis methods by jointly encoding the intrinsic relationship of geometry and shape.
The proposed method outperforms state-of-the-art segmentation methods on the public RETOUCH dataset having images captured from different acquisition procedures.
arXiv Detail & Related papers (2020-03-31T11:50:43Z)
This list is automatically generated from the titles and abstracts of the papers in this site.
This site does not guarantee the quality of this site (including all information) and is not responsible for any consequences.