{"id":510912,"date":"2022-05-23T17:16:04","date_gmt":"2022-05-24T00:16:04","guid":{"rendered":"https:\/\/www.esri.com\/about\/newsroom\/?post_type=arcuser&#038;p=510912"},"modified":"2022-05-23T17:16:04","modified_gmt":"2022-05-24T00:16:04","slug":"micro-gis","status":"publish","type":"arcuser","link":"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis","title":{"rendered":"Expanding the\tCapabilities of Cell Image Analysis with GIS"},"author":1031,"featured_media":0,"menu_order":0,"template":"","format":"standard","meta":{"_acf_changed":false,"sync_status":"","episode_type":"","audio_file":"","podmotor_file_id":"","podmotor_episode_id":"","castos_file_data":"","cover_image":"","cover_image_id":"","duration":"","filesize":"","filesize_raw":"","date_recorded":"","explicit":"","block":"","itunes_episode_number":"","itunes_title":"","itunes_season_number":"","itunes_episode_type":"","_links_to":"","_links_to_target":""},"categories":[24962,731,91],"tags":[479312],"arcuser_issues":[479252],"class_list":["post-510912","arcuser","type-arcuser","status-publish","format-standard","hentry","category-focus","category-health","category-mapping","tag-cell-analysis","arcuser_issues-spring-2022"],"acf":{"short_description":"Researchers apply GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data.","pdf":{"host_remotely":false,"file":510922,"file_url":""},"flexible_content":[{"acf_fc_layout":"blockquote","content":"Russ Butler and Craig Gillen, along with a team of undergraduate research assistants at AdventHealth University (AHU), have been applying GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data."},{"acf_fc_layout":"content","content":"Butler and Gillen are not the first to apply GIS to analyzing the human body. Eric J. Topol, an American cardiologist, scientist, and author, proposed a human GIS in \u201cIndividualized Medicine from Prewomb to Tomb,\u201d an article published in the March 27, 2014 issue of Cell. Topol\u2019s theoretical human GIS"},{"acf_fc_layout":"image","image":510952,"image_position":"center","orientation":"horizontal","hyperlink":""},{"acf_fc_layout":"content","content":"model incorporated layers of human health information from individual biological molecules in context with environmental conditions.\r\n\r\nAccording to Butler, who is the director of the Center for Population Health Research (CPHR) at AHU, the relationship between human health and well-being corresponds to factors that range from the molecular to the global scale. \u201cWe are spatiotemporal beings, and GIS has the inherent capacity to capture these layers. GIS can provide us with a more comprehensive view of a patient for both treatment and prevention,\u201d said Butler.\r\n\r\nEmbedded in GIS systems are powerful image classification tools. These tools, in conjunction with Human GIS layers, could provide a unique way to visualize patient medical information. To augment practitioner diagnoses, imaging data such as biosensors, X-rays, MRIs, mammography, and sonograms could be classified in ways that make the data machine readable, analysis ready, and ultimately more useful.\r\n\r\nMoreover, all this information can be linked to a patient\u2019s geographic coordinates. The places where people live, work, and play are known to affect life expectancy, wellness, and health. The image classification abilities of GIS, together with its amazing capacity for almost limitless data layering and analyses from molecules to environment, could provide novel insight into understanding the complex factors determining human health and wellness.\r\nPresent-day electronic health records (EHR) systems compile extensive patient-related information. But, EHRs do not currently integrate all pertinent patient information, such as classified patient imagery and allied health notes on neighborhood characteristics, physical and occupational therapy, rehabilitation, and dietary and nutrition services.\r\n\r\nButler and Gillen are performing spatial analyses at the micro-GIS level by modeling cellular distributions to better understand Mycobacterium tuberculosis\u2014the bacteria that causes tuberculosis (TB)\u2014a disease that has infected humans for millennia. The World Health Organization (WHO) noted that 1.5 million people died from TB in 2020, making it the second-leading infectious killer after COVID-19.\r\n\r\n\u201cTB is a difficult disease to treat. One of its intractable features is the formation of multiple cellular masses within the lungs called granulomas,\u201d said Butler. \u201cTB granulomas are small masses formed during infection that develop and grow through a dynamic process between the host immune response and mycobacteria. It is well-known that granuloma-scale outcomes, are related to disease severity.\u201d\r\n\r\nResearchers used knowledge gained through these runs and applied it to unsupervised runs. These classifications produced subsequent category collapsing to identify the desired cell types.\r\n\r\n\u201cThis is a very complex process where human input and machine classifications are iterative, with the human input the final arbiter,\u201d said Butler. \u201cFor example, unlike, say, a forest classified from satellite imagery, our images have depth.\u201d A tissue section of a cell could be angled from deep in the cell to its surface, which would vary the expression of staining.\r\n\r\nThis process is much more complex than classifying a forest on a slope because the samples the team works with\u2014tissue, intracellular matrix, or other cells\u2014are more difficult to handle. As a result, Butler noted that, \u201cIt is virtually impossible to produce an undamaged tissue sample that is only one cell thick. We have been working on this for five years now and appreciate the advice and support that Esri staff members have provided us.\u201d\r\n\r\nExtending the micro-GIS capabilities for cell image analysis to human imaging modalities, such as X-ray, MRI, CT scans, and ultrasound\u2014when combined with immunology, microbiology, histology, and\/or epidemiology\u2014could lead to a significant reduction of the global burden of disease concluded Butler.\r\n\r\n&nbsp;"},{"acf_fc_layout":"image","image":510962,"image_position":"left","orientation":"horizontal","hyperlink":""},{"acf_fc_layout":"content","content":"Using micro-GIS to quantitatively assess granuloma structure, Butler believes this research can significantly contribute to understanding TB and lead to better treatment outcomes. Butler, in collaboration with researchers from the University of Michigan and the University of Pittsburgh, has published several papers about the use of micro-GIS to examine granulomas.\r\n\r\n\u201cUsing the power of ArcGIS classification algorithms and by applying Cartesian coordinate systems, we are among the very first to create a novel pipeline for spatioquantitatively defined cellular patterns within granulomas,\u201d said Butler. Several different image classification techniques were used\u2014support vector machine (SVM) and random tree\u2014on a variety of granuloma images. These supervised machine learning techniques require training sample files. These training files were created by selecting as many as 100 sample sites of the different cell types.\r\n\r\nResearchers were interested in two to three different cell types for any given image or project. The analysis used geoprocessing tools, often the Classification Wizard, to produce classified images that provided feedback about the distributions of different cell types.\r\n\r\nThis also showed that staining techniques often resulted in cellular debris being misclassified as cells. The use of geoprocessing tools helped to develop an unsupervised classification process, which greatly helped separate stained cells from merely stained cytoplasm. Classified images compared to the same stained biological samples revealed the cellular nuclei."}],"references":null},"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v25.9 (Yoast SEO v25.9) - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Mapping TB cells with GIS<\/title>\n<meta name=\"description\" content=\"Russ Butler and Craig Gillen, along with a team of undergraduate research assistants at AdventHealth University (AHU), studying tuberculosis by applying GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Expanding the Capabilities of Cell Image Analysis with GIS\" \/>\n<meta property=\"og:description\" content=\"Russ Butler and Craig Gillen, along with a team of undergraduate research assistants at AdventHealth University (AHU), studying tuberculosis by applying GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis\" \/>\n<meta property=\"og:site_name\" content=\"Esri\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/esrigis\/\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.esri.com\/about\/newsroom\/app\/uploads\/2022\/05\/micro_GIS_banner.jpg\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@Esri\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\n\t    \"@context\": \"https:\/\/schema.org\",\n\t    \"@graph\": [\n\t        {\n\t            \"@type\": \"WebPage\",\n\t            \"@id\": \"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis\",\n\t            \"url\": \"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis\",\n\t            \"name\": \"Mapping TB cells with GIS\",\n\t            \"isPartOf\": {\n\t                \"@id\": \"https:\/\/www.esri.com\/about\/newsroom\/#website\"\n\t            },\n\t            \"datePublished\": \"2022-05-24T00:16:04+00:00\",\n\t            \"description\": \"Russ Butler and Craig Gillen, along with a team of undergraduate research assistants at AdventHealth University (AHU), studying tuberculosis by applying GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data.\",\n\t            \"breadcrumb\": {\n\t                \"@id\": \"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis#breadcrumb\"\n\t            },\n\t            \"inLanguage\": \"en-US\",\n\t            \"potentialAction\": [\n\t                {\n\t                    \"@type\": \"ReadAction\",\n\t                    \"target\": [\n\t                        \"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis\"\n\t                    ]\n\t                }\n\t            ]\n\t        },\n\t        {\n\t            \"@type\": \"BreadcrumbList\",\n\t            \"@id\": \"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis#breadcrumb\",\n\t            \"itemListElement\": [\n\t                {\n\t                    \"@type\": \"ListItem\",\n\t                    \"position\": 1,\n\t                    \"name\": \"Home\",\n\t                    \"item\": \"https:\/\/www.esri.com\/about\/newsroom\"\n\t                },\n\t                {\n\t                    \"@type\": \"ListItem\",\n\t                    \"position\": 2,\n\t                    \"name\": \"Expanding the Capabilities of Cell Image Analysis with GIS\"\n\t                }\n\t            ]\n\t        },\n\t        {\n\t            \"@type\": \"WebSite\",\n\t            \"@id\": \"https:\/\/www.esri.com\/about\/newsroom\/#website\",\n\t            \"url\": \"https:\/\/www.esri.com\/about\/newsroom\/\",\n\t            \"name\": \"Esri\",\n\t            \"description\": \"Esri Newsroom\",\n\t            \"potentialAction\": [\n\t                {\n\t                    \"@type\": \"SearchAction\",\n\t                    \"target\": {\n\t                        \"@type\": \"EntryPoint\",\n\t                        \"urlTemplate\": \"https:\/\/www.esri.com\/about\/newsroom\/?s={search_term_string}\"\n\t                    },\n\t                    \"query-input\": {\n\t                        \"@type\": \"PropertyValueSpecification\",\n\t                        \"valueRequired\": true,\n\t                        \"valueName\": \"search_term_string\"\n\t                    }\n\t                }\n\t            ],\n\t            \"inLanguage\": \"en-US\"\n\t        },\n\t        {\n\t            \"@type\": \"Person\",\n\t            \"@id\": \"https:\/\/www.esri.com\/about\/newsroom\/#\/schema\/person\/82e5143bcdebadf8fd64d84e503ca468\",\n\t            \"name\": \"Monica Pratt\",\n\t            \"image\": {\n\t                \"@type\": \"ImageObject\",\n\t                \"inLanguage\": \"en-US\",\n\t                \"@id\": \"https:\/\/www.esri.com\/about\/newsroom\/#\/schema\/person\/image\/\",\n\t                \"url\": \"https:\/\/www.esri.com\/about\/newsroom\/app\/uploads\/2018\/08\/MonicaMug_agol2.jpg\",\n\t                \"contentUrl\": \"https:\/\/www.esri.com\/about\/newsroom\/app\/uploads\/2018\/08\/MonicaMug_agol2.jpg\",\n\t                \"caption\": \"Monica Pratt\"\n\t            },\n\t            \"description\": \"Monica Pratt is the founding and current editor of ArcUser magazine, the executive editor of ArcNews magazine, the editor of Esri Globe and head of the Publications team at Esri. She has been writing on technology topics, specializing in GIS, for more than 30 years. Before joining Esri in 1997, she worked for newspapers and in the financial industry.\",\n\t            \"sameAs\": [\n\t                \"https:\/\/x.com\/ArcUser\"\n\t            ],\n\t            \"url\": \"\"\n\t        }\n\t    ]\n\t}<\/script>\n<!-- \/ Yoast SEO Premium plugin. -->","yoast_head_json":{"title":"Mapping TB cells with GIS","description":"Russ Butler and Craig Gillen, along with a team of undergraduate research assistants at AdventHealth University (AHU), studying tuberculosis by applying GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data.","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis","og_locale":"en_US","og_type":"article","og_title":"Expanding the Capabilities of Cell Image Analysis with GIS","og_description":"Russ Butler and Craig Gillen, along with a team of undergraduate research assistants at AdventHealth University (AHU), studying tuberculosis by applying GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data.","og_url":"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis","og_site_name":"Esri","article_publisher":"https:\/\/www.facebook.com\/esrigis\/","og_image":[{"url":"https:\/\/www.esri.com\/about\/newsroom\/app\/uploads\/2022\/05\/micro_GIS_banner.jpg","type":"","width":"","height":""}],"twitter_card":"summary_large_image","twitter_site":"@Esri","schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"WebPage","@id":"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis","url":"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis","name":"Mapping TB cells with GIS","isPartOf":{"@id":"https:\/\/www.esri.com\/about\/newsroom\/#website"},"datePublished":"2022-05-24T00:16:04+00:00","description":"Russ Butler and Craig Gillen, along with a team of undergraduate research assistants at AdventHealth University (AHU), studying tuberculosis by applying GIS technology on the micro scale to add image classification to spatiotemporally stamped human health data.","breadcrumb":{"@id":"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis#breadcrumb"},"inLanguage":"en-US","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis"]}]},{"@type":"BreadcrumbList","@id":"https:\/\/www.esri.com\/about\/newsroom\/arcuser\/micro-gis#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.esri.com\/about\/newsroom"},{"@type":"ListItem","position":2,"name":"Expanding the Capabilities of Cell Image Analysis with GIS"}]},{"@type":"WebSite","@id":"https:\/\/www.esri.com\/about\/newsroom\/#website","url":"https:\/\/www.esri.com\/about\/newsroom\/","name":"Esri","description":"Esri Newsroom","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.esri.com\/about\/newsroom\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-US"},{"@type":"Person","@id":"https:\/\/www.esri.com\/about\/newsroom\/#\/schema\/person\/82e5143bcdebadf8fd64d84e503ca468","name":"Monica Pratt","image":{"@type":"ImageObject","inLanguage":"en-US","@id":"https:\/\/www.esri.com\/about\/newsroom\/#\/schema\/person\/image\/","url":"https:\/\/www.esri.com\/about\/newsroom\/app\/uploads\/2018\/08\/MonicaMug_agol2.jpg","contentUrl":"https:\/\/www.esri.com\/about\/newsroom\/app\/uploads\/2018\/08\/MonicaMug_agol2.jpg","caption":"Monica Pratt"},"description":"Monica Pratt is the founding and current editor of ArcUser magazine, the executive editor of ArcNews magazine, the editor of Esri Globe and head of the Publications team at Esri. She has been writing on technology topics, specializing in GIS, for more than 30 years. Before joining Esri in 1997, she worked for newspapers and in the financial industry.","sameAs":["https:\/\/x.com\/ArcUser"],"url":""}]}},"sort_order":"18","_links":{"self":[{"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/arcuser\/510912","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/arcuser"}],"about":[{"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/types\/arcuser"}],"author":[{"embeddable":true,"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/users\/1031"}],"version-history":[{"count":0,"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/arcuser\/510912\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/media?parent=510912"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/categories?post=510912"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/tags?post=510912"},{"taxonomy":"arcuser_issues","embeddable":true,"href":"https:\/\/www.esri.com\/about\/newsroom\/wp-json\/wp\/v2\/arcuser_issues?post=510912"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}