Abstract Doctors typically use non‐contrast‐enhanced computed tomography (NCECT) in the treatment of kidney cancer to map kidney and tumour structural information to functional imaging single‐photon emission computed tomography, which is then used to assess patient kidney function and predict postoperative recovery. However, the assessment of kidney function and formulation of surgical plans is constrained by the low contrast of tumours in NCECT, which hinders the acquisition of accurate tumour boundaries. Therefore, this study designed a radiomics feature‐enhanced level‐set evolution (RFLSE) to precisely segment small‐sample low‐contrast kidney tumours. Integration of high‐dimensional radiomics features into the level‐set energy function enhances the edge detection capability of low‐contrast kidney tumours. The use of sensitive radiomics features to control the regional term parameters achieves adaptive adjustment of the curve evolution amplitude, improving the level‐set segmentation process. The experimental data used low‐contrast, limited‐sample tumours provided by hospitals, as well as the public datasets BUSI18 and KiTS19. Comparative results with advanced energy functionals and deep learning models demonstrate the precision and robustness of RFLSE segmentation. Additionally, the application value of RFLSE in assisting doctors with accurately marking tumours and generating high‐quality pseudo‐labels for deep learning datasets is demonstrated.

MOTIVATION: The emerging single-cell Hi-C technology provides opportunities to study dynamics of chromosomal organization. How to construct a pseudotime path using single-cell Hi-C contact matrices to order cells along developmental trajectory is a challenging topic, since these matrices produced by the technology are inherently high dimensional and sparse, they suffer from noises and biases, and the topology of trajectory underlying them may be diverse. RESULTS: We present scHiCPTR, an unsupervised graph-based pipeline to infer pseudotime from single-cell Hi-C contact matrices. It provides a workflow consisting of imputation and embedding, graph construction, dual graph refinement, pseudotime calculation and result visualization. Beyond the few existing methods, scHiCPTR ties to optimize graph structure by two parallel procedures of graph pruning, which help reduce the spurious cell links resulted from noises and determine a global developmental directionality. Besides, it has an ability to handle developmental trajectories with multiple topologies, including linear, bifurcated and circular ones, and is competitive with methods developed for single-cell RNA-seq data. The comparative results tell that our scHiCPTR can achieve higher performance in pseudotime inference, and the inferred developmental trajectory exhibit a reasonable biological significance. AVAILABILITY AND IMPLEMENTATION: scHiCPTR is freely available at https://github.com/lhqxinghun/scHiCPTR. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.