Khatun, Rupali
SMILE-UHURA Challenge -- Small Vessel Segmentation at Mesoscopic Scale from Ultra-High Resolution 7T Magnetic Resonance Angiograms
Chatterjee, Soumick, Mattern, Hendrik, Dörner, Marc, Sciarra, Alessandro, Dubost, Florian, Schnurre, Hannes, Khatun, Rupali, Yu, Chun-Chih, Hsieh, Tsung-Lin, Tsai, Yi-Shan, Fang, Yi-Zeng, Yang, Yung-Ching, Huang, Juinn-Dar, Xu, Marshall, Liu, Siyu, Ribeiro, Fernanda L., Bollmann, Saskia, Chintalapati, Karthikesh Varma, Radhakrishna, Chethan Mysuru, Kumara, Sri Chandana Hudukula Ram, Sutrave, Raviteja, Qayyum, Abdul, Mazher, Moona, Razzak, Imran, Rodero, Cristobal, Niederren, Steven, Lin, Fengming, Xia, Yan, Wang, Jiacheng, Qiu, Riyu, Wang, Liansheng, Panah, Arya Yazdan, Jurdi, Rosana El, Fu, Guanghui, Arslan, Janan, Vaillant, Ghislain, Valabregue, Romain, Dormont, Didier, Stankoff, Bruno, Colliot, Olivier, Vargas, Luisa, Chacón, Isai Daniel, Pitsiorlas, Ioannis, Arbeláez, Pablo, Zuluaga, Maria A., Schreiber, Stefanie, Speck, Oliver, Nürnberger, Andreas
The human brain receives nutrients and oxygen through an intricate network of blood vessels. Pathology affecting small vessels, at the mesoscopic scale, represents a critical vulnerability within the cerebral blood supply and can lead to severe conditions, such as Cerebral Small Vessel Diseases. The advent of 7 Tesla MRI systems has enabled the acquisition of higher spatial resolution images, making it possible to visualise such vessels in the brain. However, the lack of publicly available annotated datasets has impeded the development of robust, machine learning-driven segmentation algorithms. To address this, the SMILE-UHURA challenge was organised. This challenge, held in conjunction with the ISBI 2023, in Cartagena de Indias, Colombia, aimed to provide a platform for researchers working on related topics. The SMILE-UHURA challenge addresses the gap in publicly available annotated datasets by providing an annotated dataset of Time-of-Flight angiography acquired with 7T MRI. This dataset was created through a combination of automated pre-segmentation and extensive manual refinement. In this manuscript, sixteen submitted methods and two baseline methods are compared both quantitatively and qualitatively on two different datasets: held-out test MRAs from the same dataset as the training data (with labels kept secret) and a separate 7T ToF MRA dataset where both input volumes and labels are kept secret. The results demonstrate that most of the submitted deep learning methods, trained on the provided training dataset, achieved reliable segmentation performance. Dice scores reached up to 0.838 $\pm$ 0.066 and 0.716 $\pm$ 0.125 on the respective datasets, with an average performance of up to 0.804 $\pm$ 0.15.
Machine learning approach for segmenting glands in colon histology images using local intensity and texture features
Khatun, Rupali, Chatterjee, Soumick
Colon Cancer is one of the most common types of cancer. The treatment is planned to depend on the grade or stage of cancer. One of the preconditions for grading of colon cancer is to segment the glandular structures of tissues. Manual segmentation method is very time-consuming, and it leads to life risk for the patients. The principal objective of this project is to assist the pathologist to accurate detection of colon cancer. In this paper, the authors have proposed an algorithm for an automatic segmentation of glands in colon histology using local intensity and texture features. Here the dataset images are cropped into patches with different window sizes and taken the intensity of those patches, and also calculated texture-based features. Random forest classifier has been used to classify this patch into different labels. A multilevel random forest technique in a hierarchical way is proposed. This solution is fast, accurate and it is very much applicable in a clinical setup.