Chelebian, E. | bioRxiv Science

bioRxiv2022

TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics data

Background and ObjectivesSpatially resolved techniques for exploring the molecular landscape of tissue samples, such as spatial transcriptomics, often result in millions of data points and images too large to view on a regular desktop computer, limiting the possibilities in visual interactive data exploration. TissUUmaps is a free, open-source browser-based tool for GPU-accelerated visualization and interactive exploration of 107+ data points overlaying tissue samples. MethodsHerein we describe how TissUUmaps 3 provides instant multiresolution image viewing and can be customized, shared, and also integrated into Jupyter Notebooks. We introduce new modules where users can visualize markers and regions, explore spatial statistics, perform quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. ResultsWe show that thanks to targeted optimizations the time and cost associated with interactive data exploration were reduced, enabling TissUUmaps 3 to handle the scale of todays spatial transcriptomics methods. ConclusionTissUUmaps 3 provides significantly improved performance for large multiplex datasets as compared to previous versions. We envision TissUUmaps to contribute to broader dissemination and flexible sharing of large-scale spatial omics data.

bioinformatics↗

bioRxiv2020

Higher vascularity at infiltrated peripheral edema differentiates proneural glioblastoma subtype

BACKGROUND AND PURPOSEGenetic classifications are crucial for understanding the heterogeneity of glioblastoma. Recently, MR perfusion imaging techniques have demonstrated their ability to determine molecular alterations. In this work, we investigated whether perfusion markers within infiltrated peripheral edema were associated with proneural, mesenchymal, classical and neural subtypes. MATERIALS AND METHODSONCOhabitats open web service was used to obtain the cerebral blood volume at the infiltrated peripheral edema for MRI studies of 50 glioblastoma patients from The Cancer Imaging Archive: TCGA-GBM. ANOVA and Kruskal-Wallis tests were carried out in order to assess the association between vascular features and the subtypes. For assessing specific differences, Mann-Whitney U-test was conducted. Finally, the association of overall survival with molecular and vascular features was assessed using univariate and multivariate Cox models. RESULTSANOVA and Kruskal-Wallis tests for the maximum cerebral blood volume at the infiltrated peripheral edema between the four subclasses yielded false discovery rate corrected p-values of <0.001 and 0.02, respectively. This vascular feature was significantly higher (p=0.0043) in proneural patients compared to the rest of the subtypes while conducting Mann-Whitney U-test. The multivariate Cox model pointed to redundant information provided by vascular features at the peripheral edema and proneural subtype when analyzing overall survival. CONCLUSIONSHigher relative cerebral blood volume at infiltrated peripheral edema is associated with proneural glioblastoma subtype suggesting underlying vascular behavior related to molecular composition in that area.

neuroscience↗