{"id":6127,"date":"2026-08-19T15:32:18","date_gmt":"2026-08-19T08:32:18","guid":{"rendered":"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/?p=6127"},"modified":"2026-08-19T16:06:36","modified_gmt":"2026-08-19T09:06:36","slug":"crisp-a-deep-learning-architecture-for-gc-x-gc-tofms-contour-roi-identification-simulation-and-analysis-in-imaging-metabolomics","status":"publish","type":"post","link":"https:\/\/www2.si.mahidol.ac.th\/department\/biochemistry\/crisp-a-deep-learning-architecture-for-gc-x-gc-tofms-contour-roi-identification-simulation-and-analysis-in-imaging-metabolomics\/","title":{"rendered":"CRISP: a deep learning architecture for GC \u00d7 GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics"},"content":{"rendered":"<p>Vivek Bhakta Mathema, Kassaporn Duangkumpha, Kwanjeera Wanichthanarak, Narumol Jariyasopit, Esha Dhakal, Nuankanya Sathirapongsasuti, Chagriya Kitiyakara, Yongyut Sirivatanauksorn, <strong>Sakda Khoomrung<\/strong><\/p>\n<h2 class=\"title\">Abstract<\/h2>\n<div id=\"eng-abstract\" class=\"abstract-content selected\">\n<div class=\"title\">\n<p>Two-dimensional gas chromatography-time-of-flight mass spectrometry (GC \u00d7 GC-TOFMS) provides a large amount of molecular information from biological samples. However, the lack of a comprehensive compound library or customizable bioinformatics tool is currently a challenge in GC \u00d7 GC-TOFMS data analysis. We present an open-source deep learning (DL) software called contour regions of interest (ROI) identification, simulation and untargeted metabolomics profiler (CRISP). CRISP integrates multiple customizable deep neural network architectures for assisting the semi-automated identification of ROIs, contour synthesis, resolution enhancement and classification of GC \u00d7 GC-TOFMS-based contour images. The approach includes the novel aggregate feature representative contour (AFRC) construction and stacked ROIs. This generates an unbiased contour image dataset that enhances the contrasting characteristics between different test groups and can be suitable for small sample sizes. The utility of the generative models and the accuracy and efficacy of the platform were demonstrated using a dataset of GC \u00d7 GC-TOFMS contour images from patients with late-stage diabetic nephropathy and healthy control groups. CRISP successfully constructed AFRC images and identified over five ROIs to create a deepstacked dataset. The high fidelity, 512 \u00d7 512-pixels generative model was trained as a generator with a Fr\u00e9chet inception distance of &lt;47.00. The trained classifier achieved an AUROC of &gt;0.96 and a classification accuracy of &gt;95.00% for datasets with and without column bleed. Overall, CRISP demonstrates good potential as a DL-based approach for the rapid analysis of 4-D GC \u00d7 GC-TOFMS untargeted metabolite profiles by directly implementing contour images. CRISP is available at https:\/\/github.com\/vivekmathema\/GCxGC-CRISP.<\/p>\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/35022651\/\">https:\/\/pubmed.ncbi.nlm.nih.gov\/35022651\/<\/a><\/p>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Vivek Bhakta Mathema, Kassaporn Duangkumpha, Kwanjeera  [&#8230;]\n","protected":false},"author":6,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[3],"tags":[],"class_list":["post-6127","post","type-post","status-publish","format-standard","hentry","category-3"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>CRISP: a deep learning architecture for GC \u00d7 GC-TOFMS contour ROI identification, simulation and analysis in imaging metabolomics - \u0e20\u0e32\u0e04\u0e27\u0e34\u0e0a\u0e32\u0e0a\u0e35\u0e27\u0e40\u0e04\u0e21\u0e35 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