Dataset Information

Spa-RQ: an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer.

ABSTRACT: To facilitate analysis of spatial tissue phenotypes, we created an open-source tool package named 'Spa-RQ' for 'Spatial tissue analysis: image Registration & Quantification'. Spa-RQ contains software for image registration (Spa-R) and quantitative analysis of DAB staining overlap (Spa-Q). It provides an easy-to-implement workflow for serial sectioning and staining as an alternative to multiplexed techniques. To demonstrate Spa-RQ's applicability, we analysed the spatial aspects of oncogenic KRAS-related signalling activities in non-small cell lung cancer (NSCLC). Using Spa-R in conjunction with ImageJ/Fiji, we first performed annotation-guided tumour-by-tumour phenotyping using multiple signalling markers. This analysis showed histopathology-selective activation of PI3K/AKT and MAPK signalling in Kras mutant murine tumours, as well as high p38MAPK stress signalling in p53 null murine NSCLC. Subsequently, Spa-RQ was applied to measure the co-activation of MAPK, AKT, and their mutual effector mTOR pathway in individual tumours. Both murine and clinical NSCLC samples could be stratified into 'MAPK/mTOR', 'AKT/mTOR', and 'Null' signature subclasses, suggesting mutually exclusive MAPK and AKT signalling activities. Spa-RQ thus provides a robust and easy to use tool that can be employed to identify spatially-distributed tissue phenotypes.

SUBMITTER: Bao J

PROVIDER: S-EPMC6879493 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

Spa-RQ: an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer.

Bao Jie J Walliander Margarita M Kovács Ferenc F Nagaraj Ashwini S AS Hemmes Annabrita A Sarhadi Virinder Kaur VK Knuutila Sakari S Lundin Johan J Horvath Peter P Verschuren Emmy W EW

Scientific reports 20191126 1

To facilitate analysis of spatial tissue phenotypes, we created an open-source tool package named 'Spa-RQ' for 'Spatial tissue analysis: image Registration & Quantification'. Spa-RQ contains software for image registration (Spa-R) and quantitative analysis of DAB staining overlap (Spa-Q). It provides an easy-to-implement workflow for serial sectioning and staining as an alternative to multiplexed techniques. To demonstrate Spa-RQ's applicability, we analysed the spatial aspects of oncogenic KRAS ...[more]

PMID: 31772293

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Project description:BackgroundMagnetic resonance imaging (MRI) is uniquely suited to non-invasively and continuously monitor embolism formation in trees. Depending on the MRI method used, quantitative parameter maps of water content and MRI signal relaxation behavior can be generated. The ability to measure dynamic differences in water content and relaxation behavior can be used to detect xylem embolism formation, even if xylem conduits are too small to be spatially resolved. This is especially advantageous when using affordable small-scale low-field MRI scanners. The amount of signal that can be obtained from an object strongly depends on the strength of the magnetic field of the imager's magnet. Imaging at lower resolutions thus would allow to reduce the cost, size and weight of the MRI scanner and to shorten image acquisition times.ResultsWe investigated how much spatial resolution can be sacrificed without losing the ability to monitor embolism formation in coniferous softwood (spruce, Picea abies) and diffuse porous beech (Fagus sylvatica). Saplings of both species were bench dehydrated, while they were continuously imaged at stepwise decreasing spatial resolutions. Imaging was done by means of a small-scale MRI device, utilizing image matrix sizes of 128 × 128, 64 × 64 and 32 × 32 pixels at a constant FOV of 19 and 23 mm, respectively. While images at the lowest resolutions (pixel sizes 0.59 × 0.59 mm and 0.72 × 0.72 mm) were no longer sufficient to resolve finer details of the stem anatomy, they did permit an approximate localization of embolism formation and the generation of accurate vulnerability curves.ConclusionsWhen using MRI, spatial resolution can be sacrificed without losing the ability to visualize and quantify embolism formation. Imaging at lower spatial resolution to monitor embolism formation has two advantages. Firstly, the acquisition time per image can be reduced dramatically. This enables continuous imaging at high time resolution, which may be beneficial to monitor rapid dynamics of embolism formation. Secondly, if the requirements for spatial resolution are relaxed, much simpler MRI devices can be used. This has the potential to make non-invasive MR imaging of embolism formation much more affordable and more widely available.

Dataset Information

Spa-RQ: an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer.

Publications

Spa-RQ: an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer.

Similar Datasets

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