CINXE.COM

HALO® image analysis platform | In Situ Hybridization, RNA-ISH | ACDBio

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src="https://acdbio.com/sites/default/files/products-banner_0.jpg" class="img-banner"><h1 class="general-title">HALO<sup>®</sup> image analysis platform</h1></div><div class="content-container container"><div class="region region-content"><div id="block-system-main" class="block block-system clearfix"><div class="content"><div id="node-20227" class="node node-product-sub-category page-node- node-type-product-category" about="/halo-image-analysis-platform" typeof="sioc:Item foaf:Document"><div class="nav-tab-container"><ul class="nav nav-tabs page-tabs" id="myTab"><li><a href="/analysis-software">Overview</a></li><li class="pro-category-115267" ><a href="/aperio-rna-ish-algorithm">Aperio RNA ISH Algorithm</a></li><li class="active pro-category-20227"><a href="/halo-image-analysis-platform" class="active">HALO<sup>®</sup> image analysis platform</a></li></ul></div><div class="tab-content"><div id="tab0" class="tab-pane fade in active profile"><div class="sample-image"><div class="profile-content"><h3>HALO<sup>®</sup> image analysis platform</h3></div><div class="loader-image-gallery"></div><div id="film_roll" class="sample-slider"><div><img typeof="foaf:Image" src="https://acdbio.com/sites/default/files/styles/sample_image/public/Position%201.png" width="765" height="451" alt="HALO 3.3 user interface displaying the results section. The left panel includes summary analysis data, histograms, and cell-by-cell data. A cell of interest is highlighted in both the cell table and the image. Enlarged histogram displayed in middle." /><p class="slider-below-text"> HALO 3.3 user interface displaying the results section. The left panel includes summary analysis data, histograms, and cell-by-cell data. A cell of interest is highlighted in both the cell table and the image. Enlarged histogram displayed in middle.</p></div><div><img typeof="foaf:Image" src="https://acdbio.com/sites/default/files/styles/sample_image/public/Position%202.jpg" width="765" height="451" alt="BaseScope analysis using the HALO ISH module. (A) PPIB positive control shown with HALO mark-up image in (B). (C) KRAS assay shown with mark-up in (D). In the mark-up images, cells with probes are shown in varying shades of green with darker cells having more probes. White cells have no probes or a number below the minimum number defined by the user." /><p class="slider-below-text"> BaseScope analysis using the HALO ISH module. (A) PPIB positive control shown with HALO mark-up image in (B). (C) KRAS assay shown with mark-up in (D). In the mark-up images, cells with probes are shown in varying shades of green with darker cells having more probes. White cells have no probes or a number below the minimum number defined by the user.</p></div><div><img typeof="foaf:Image" src="https://acdbio.com/sites/default/files/styles/sample_image/public/Position%203.jpg" width="765" height="451" alt="Duplex FISH assay analyzed with the FISH module of HALO. (A) Duplex FISH assay with nuclei in blue, probe 1 in green, and probe 2 in magenta. (B) HALO FISH analysis mark-up image, where cyan nuclei represent cyan probe positivity and cyan spots represent probes. Similarly, green nuclei represent green probe positivity and green spots represent the green probe. Purple nuclei represent dual positivity." /><p class="slider-below-text"> Duplex FISH assay analyzed with the FISH module of HALO. (A) Duplex FISH assay with nuclei in blue, probe 1 in green, and probe 2 in magenta. (B) HALO FISH analysis mark-up image, where cyan nuclei represent cyan probe positivity and cyan spots represent probes. Similarly, green nuclei represent green probe positivity and green spots represent the green probe. Purple nuclei represent dual positivity.</p></div><div><img typeof="foaf:Image" src="https://acdbio.com/sites/default/files/styles/sample_image/public/Position%204.jpg" width="765" height="451" alt="Co-detection assay using the ISH-IHC module of HALO. (A) ISH-IHC assay with a magenta probe and a teal protein biomarker. (B) HALO mark-up image where blue represents nuclei without probe and lime green represents positivity for the teal IHC biomarker. The pink spots represent the magenta probe, and the gray rings represent a user defined maximum cytoplasmic radius." /><p class="slider-below-text"> Co-detection assay using the ISH-IHC module of HALO. (A) ISH-IHC assay with a magenta probe and a teal protein biomarker. (B) HALO mark-up image where blue represents nuclei without probe and lime green represents positivity for the teal IHC biomarker. The pink spots represent the magenta probe, and the gray rings represent a user defined maximum cytoplasmic radius.</p></div><div><img typeof="foaf:Image" src="https://acdbio.com/sites/default/files/styles/sample_image/public/Position%205.jpg" width="765" height="451" alt="Spatial analysis of RNAscope data. (A) An ISH-IHC assay with magenta ISH probe and blue protein. (B) A Density Heatmap is shown of a single-plex magenta ISH probe where blue represents areas of low expression and red represents areas of highest expression." /><p class="slider-below-text"> Spatial analysis of RNAscope data. (A) An ISH-IHC assay with magenta ISH probe and blue protein. (B) A Density Heatmap is shown of a single-plex magenta ISH probe where blue represents areas of low expression and red represents areas of highest expression.</p></div><div><img typeof="foaf:Image" src="https://acdbio.com/sites/default/files/styles/sample_image/public/Position%206.png" width="765" height="451" alt="HALO offers a variety of image analysis export options including exporting cell-by-cell data, summary data, and summary reports, as shown above." /><p class="slider-below-text"> HALO offers a variety of image analysis export options including exporting cell-by-cell data, summary data, and summary reports, as shown above.</p></div></div><style type="text/css"> .loader-image-gallery { position: absolute; left: 0px; top: 0px; width: 100%; height: 100%; z-index: 9999; background: url('/sites/default/files/loading_apple.gif') 50% 35% no-repeat rgb(249,249,249); background-size: 100px; opacity: .8; } .sample-image { position: relative; } </style> <script type="text/javascript"> jQuery(document).ready(function($) { // $('#film_roll').hide(); function preloader(){ $('.loader-image-gallery').hide(); $('#film_roll').show(); } window.onload = preloader; }); </script> <div class="profile-content"> <article class="read-more"><div class="field field-name-body field-type-text-with-summary field-label-hidden"><div class="field-items"><div class="field-item even" property="content:encoded"><p> ACD has partnered with Indica Labs to offer quantitative RNAscope image analysis. HALO is an easy-to-use digital pathology image analysis platform that brings objective and accurate quantification to RNA<em> in situ</em> hybridization, enabling a new generation of applications based  on single-cell analysis.</p><p>With the purpose-built <a href="https://indicalab.com/products/sish-dual-cish-quantification/" target="_blank">ISH</a>, <a href="https://indicalab.com/products/ish-ihc-quantification/" target="_blank">ISH-IHC</a>, <a href="https://indicalab.com/products/multiplex-fish/" target="_blank">FISH</a>, and <a href="https://indicalab.com/products/fish-if-quantification" target="_blank">FISH-IF</a> modules of the <a href="https://indicalab.com/halo/" target="_blank">HALO<sup>®</sup></a> image analysis platform, pathologists and researchers can perform quantitative gene expression analysis at single-cell resolution across whole slide images, interpret data in the histopathological context and create publication quality figures in minutes.</p></div></div></div> </article></div><div class="profile-bottom"><p>RNAscope quantification with HALO provides:</p><ul><li>Quantitative and reproducible RNAscope spot counting</li><li>Single-plex and multiplex ISH quantification</li><li>Brightfield and fluorescent ISH quantification</li><li>Cell-by-cell expression profiles</li><li>Automatic generation of H-scores and histograms</li><li>Rapid whole-slide analysis</li><li>Manual and automatic selection of distinct cell populations</li><li>Proximity Analysis, Nearest Neighbor Analysis, Infiltration Analysis, and Density Heatmap are available with the <a href="https://indicalab.com/products/spatial-analysis-2/" target="_blank">Spatial Analysis module</a></li></ul><p>&nbsp;</p><div class="row review app-note"><div class="col-md-4"><img src="/sites/default/files/IndicaLabs_ACD_WP2022_shadow.jpg" style="max-width: 100%;" /></div><div class="col-md-8 download-pdf"><h3>Quantitative RNAscope Image Analysis Guide</h3><a class="down-pdf-btn learn-more" href="/system/files_force/Quantitative_RNAscope_Image_Analysis_Guide.pdf?download=1">Download App Note</a></div><div class="clear">&nbsp;</div></div><p>&nbsp;</p><p>The <a href="https://indicalab.com/halo/" target="_blank">HALO image analysis platform</a> is compatible with all RNAscope Manual and Automated Assays:</p><ul><li>RNAscope 2.5 HD Reagent Kit—BROWN</li><li>RNAscope 2.5 HD Reagent Kit—RED</li><li>RNAscope 2.5 LS Duplex Assay</li><li>RNAscope 2.5 LS Fluorescent Multiplex Assay</li><li>RNAscope 2.5 &nbsp;LSx Reagent Kit—BROWN</li><li>RNAscope 2.5 LSx Reagent Kit—RED</li><li>BaseScope LS Reagent Kit —RED</li><li>miRNAscope LS Reagent Kit Red</li><li>RNAscope VS Universal HRP</li><li>RNAscope VS Universal AP</li><li>RNAscope VS Duplex Assay</li><li>BaseScope VS Reagent Kit —RED</li><li>RNA-Protein Co-detection Ancillary Kit</li><li>DNAscope Duplex Assay</li></ul><p>&nbsp;</p><p>ACD offers image analysis as part of our Professional Assay Services (Learn more).</p><p>&nbsp;</p><p>The <a href="https://indicalab.com/halo/" target="_blank">HALO image analysis platform</a> is also available for purchase and deployment within your organization. For more information contact <a href="mailto:info@indicalab.com" target="_blank">info@indicalab.com</a>.</p></div></div></div></div></div> <script type="text/javascript"> jQuery(document).ready(function($) { $('.nomen-content').hide(); $('.nomen-tabs li').hover(function() { $('.nomen-content').show(); $(this).addClass('active'); $('.nomen-content > div').removeClass('active'); $('.nomen-content #'+$(this).attr('key')).addClass('active'); }, function() { $('.nomen-content').hide(); $('.nomen-tabs li').removeClass('active'); }); $('.nomen-content').hover(function() { $(this).show(); $('li[key='+$(this).children('div.active').attr('id')+']').addClass('active'); }, function() { $(this).hide(); $('.nomen-tabs li').removeClass('active'); }); $('.learn-more-pardot').click(function() { var left = ($(window).width()/2)-(800/2), top = ($(window).height()/2)-(800/2), NWin = window.open($(this).prop('href'), '', 'height=800, width=800, top='+top+', left='+left); if (window.focus) { NWin.focus(); } return false; 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Phone Number", company: "Please enter your Institution/Company", case_captcha: "Please Enter Valid Captcha." }, submitHandler: function(form) { var captchastatus = ValidCaptcha('pagecase'); //form.submit(); if(captchastatus == 'Success'){ $.ajax({ type: "POST", url: Drupal.settings.basePath + 'api/webtocase', data: { api : "obtwebtocase", fname : form.fname.value, lname : form.lname.value, email : form.email.value, phone : form.phone.value, company : form.company.value, description : form.description.value, url : form.action, }, beforeSend: function() { $('#popup-success-message').popup('show'); $('.popup-success-message .popup-loader').show(); $('.popup-success-message .popup-content').hide(); }, success: function(data){ if(data == "success"){ window.location.replace("https://acdbio.com/thank-you-contacting-acd"); }else{ $('.popup-success-message .popup-loader').hide(); $('.popup-success-message .popup-content').show(); $('.popup-success-message .popup-content 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).change(function() { var country = $(this).val(); if(country == 'US'){ $('.webform-component--city').show(); }else{ $('.edit-submitted-city').val(''); $('.webform-component--city').hide(); } }); $('.tablefield-wrapper table.tablefield.sticky-enabled.tableheader-processed.sticky-table').addClass('table'); }); </script> <style type='text/css'> .embeddedServiceHelpButton .helpButton .uiButton { background-color: #005f9e; font-family: "Arial", sans-serif; max-width: none; } .embeddedServiceHelpButton .embeddedServiceIcon::before { font-size: 2.25em; } .embeddedServiceHelpButton .helpButton .uiButton:hover { background-color: #0097ed; } .embeddedServiceHelpButton .helpButton .uiButton:focus { outline: 1px solid #005290; text-decoration: none; } .embeddedServiceHelpButton .helpButton .uiButton:active { text-decoration: none; } .embeddedServiceHelpButton .helpButton .helpButtonEnabled:hover::before, .embeddedServiceHelpButton .helpButton .helpButtonEnabled:focus::before { background-color: #0097ed; text-decoration: none; } .message { background-color: inherit; border-style: none; color: #fff; margin: 4px 20px; font-size: large; } .embeddedServiceLiveAgentStateChatHeader.alert .message { margin: 0; } .embeddedServiceLiveAgentStateChatHeader:not(.alert) .message { margin: 0; width: auto; } span#helpButtonSpan { padding: 0 50px 0 30px; } .embeddedServiceLiveAgentStateChatHeaderOption .optionName { color: #ffffff; } /* hide the URL capture field and label */ #OmniURL__c { display: none; } .prechatUI .fieldList li:nth-child(6) label { display: none; } /* Added 10px margin-top to center header text */ .headerText { margin-top: 10px; } </style> <!-- Automated_Invitation CSS --> <style type='text/css'> #snapins_invite { position: fixed !important; background-color: #FFFFFF; font-family: "Arial", sans-serif; overflow: visible; border-radius: 8px; visibility: hidden; } .embeddedServiceInvitation { background-color: transparent; max-width: 290px; max-height: 210px; -webkit-box-shadow: 0 7px 12px rgba(0, 0, 0, 0.28); -moz-box-shadow: 0 7px 12px rgba(0, 0, 0, 0.28); box-shadow: 0 7px 12px rgba(0, 0, 0, 0.28); } @media only screen and (min-width: 48em) { /*mobile*/ .embeddedServiceInvitation { max-width: 332px; max-height: 210px; } } .embeddedServiceInvitation>.embeddedServiceInvitationHeader { width: inherit; height: 48px; line-height: auto; padding: 10px; color: #FFFFFF; background-color: #005f9e; overflow: initial; display: flex; justify-content: space-between; align-items: stretch; border-top-left-radius: 8px; border-top-right-radius: 8px; } .embeddedServiceInvitationHeader #embeddedServiceAvatar { width: 32px; height: 32px; border-radius: 50%; } .embeddedServiceInvitationHeader .embeddedServiceTitleText { font-size: 18px; color: #FFFFFF; overflow: hidden; word-wrap: normal; white-space: nowrap; text-overflow: ellipsis; align-self: stretch; flex-grow: 1; max-width: 100%; margin: 0 12px; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon { background-image: none; border: none; border-radius: 3px; cursor: pointer; position: relative; bottom: 3%; background-color: transparent; width: 32px; height: 32px; font-size: 23px; color: #FFFFFF; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon:focus { outline: none; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon:focus::before { content: " "; position: absolute; top: 11%; left: 7%; width: 85%; height: 85%; background-color: rgba(255, 255, 255, 0.2); border-radius: 4px; pointer-events: none; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon:active, .embeddedServiceCloseIcon:hover { background-color: #FFFFFF; color: rgba(0, 0, 0, 0.7); opacity: 0.7; } .embeddedServiceInvitation>.embeddedServiceInvitationBody { background-color: #FFFFFF; max-height: 110px; min-width: 260px; margin: 0 8px; font-size: 14px; line-height: 20px; overflow: auto; } .embeddedServiceInvitationBody p { color: #333333; padding: 8px; margin: 12px 0; } .embeddedServiceInvitation>.embeddedServiceInvitationFooter { width: inherit; color: #FFFFFF; text-align: right; background-color: #FFFFFF; padding: 10px; max-height: none; border-bottom-left-radius: 8px; border-bottom-right-radius: 8px; margin-bottom: 10px; } .embeddedServiceInvitationFooter>.embeddedServiceActionButton { font-size: 14px; max-height: 40px; border: none; border-radius: 4px; padding: 10px; margin: 4px; text-align: center; text-decoration: none; display: inline-block; cursor: pointer; } .embeddedServiceInvitationFooter>#acceptInvite { background-image: none; background-color: #005f9e; color: #FFFFFF; } .embeddedServiceInvitationFooter>#rejectInvite { background-image: none; background-color: #FFFFFF; color: #005f9e; } </style> <!-- ...END --> <!-- Start of Invitations --> <div class="embeddedServiceInvitation" id="snapins_invite" aria-live="assertive" role="dialog" aria-atomic="true"> <div class="embeddedServiceInvitationHeader" aria-labelledby="snapins_titletext" aria-describedby="snapins_bodytext"> <img id="embeddedServiceAvatar"></img> <span class="embeddedServiceTitleText" id="snapins_titletext">Need help?</span> <button type="button" id="closeInvite" class="embeddedServiceCloseIcon" aria-label="Exit invitation">&times;</button> </div> <div class="embeddedServiceInvitationBody"> <p id="snapins_bodytext">How can we help you?</p> </div> <div class="embeddedServiceInvitationFooter" aria-describedby="snapins_bodytext"> <button type="button" class="embeddedServiceActionButton" id="rejectInvite">Close</button> <button type="button" class="embeddedServiceActionButton" id="acceptInvite">Start Chat</button> </div> </div> <style type='text/css'> #snapins_invite { background-color: #FFFFFF; font-family: "Arial", sans-serif; overflow: visible; border-radius: 8px; visibility: hidden; } .embeddedServiceInvitation { background-color: transparent; max-width: 290px; max-height: 210px; -webkit-box-shadow: 0 7px 12px rgba(0,0,0,0.28); -moz-box-shadow: 0 7px 12px rgba(0,0,0,0.28); box-shadow: 0 7px 12px rgba(0,0,0,0.28); } @media only screen and (min-width: 48em) { /*mobile*/ .embeddedServiceInvitation { max-width: 332px; max-height: 210px; } } .embeddedServiceInvitation > .embeddedServiceInvitationHeader { width: inherit; height: 32px; line-height: 32px; padding: 10px; color: #FFFFFF; background-color: #222222; overflow: initial; display: flex; justify-content: space-between; align-items: stretch; border-top-left-radius: 8px; border-top-right-radius: 8px; } .embeddedServiceInvitationHeader #embeddedServiceAvatar { width: 32px; height: 32px; border-radius: 50%; } .embeddedServiceInvitationHeader .embeddedServiceTitleText { font-size: 18px; color: #FFFFFF; overflow: hidden; word-wrap: normal; white-space: nowrap; text-overflow: ellipsis; align-self: stretch; flex-grow: 1; max-width: 100%; margin: 0 12px; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon { border: none; border-radius: 3px; cursor: pointer; position: relative; bottom: 3%; background-color: transparent; width: 32px; height: 32px; font-size: 23px; color: #FFFFFF; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon:focus { outline: none; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon:focus::before { content: " "; position: absolute; top: 11%; left: 7%; width: 85%; height: 85%; background-color: rgba(255, 255, 255, 0.2); border-radius: 4px; pointer-events: none; } .embeddedServiceInvitationHeader .embeddedServiceCloseIcon:active, .embeddedServiceCloseIcon:hover { background-color: #FFFFFF; color: rgba(0,0,0,0.7); opacity: 0.7; } .embeddedServiceInvitation > .embeddedServiceInvitationBody { background-color: #FFFFFF; max-height: 110px; min-width: 260px; margin: 0 8px; font-size: 14px; line-height: 20px; overflow: auto; } .embeddedServiceInvitationBody p { color: #333333; padding: 8px; margin: 12px 0; } .embeddedServiceInvitation > .embeddedServiceInvitationFooter { width: inherit; color: #FFFFFF; text-align: right; background-color: #FFFFFF; padding: 10px; max-height: 50px; border-bottom-left-radius: 8px; border-bottom-right-radius: 8px; } .embeddedServiceInvitationFooter > .embeddedServiceActionButton { font-size: 14px; max-height: 40px; border: none; border-radius: 4px; padding: 10px; margin: 4px; text-align: center; text-decoration: none; display: inline-block; cursor: pointer; } .embeddedServiceInvitationFooter > #acceptInvite { background-color: #005290; color: #FFFFFF; } .embeddedServiceInvitationFooter > #rejectInvite { background-color: #FFFFFF; color: #005290; } </style> <!-- doFind, doCreate and isExactMatch example for a Contact: Find a contact whose Email exactly matches the value provided by the customer in the form If there's no match, then create a Contact record and set it's First Name, Last Name, Email, and Phone to the values provided by the customer --> <!-- <input type="hidden" name="liveagent.prechat.findorcreate.map.doFind:Contact" value="Email,true" /> <input type="hidden" name="liveagent.prechat.findorcreate.map.isExactMatch:Contact" value="Email,true" /> <input type="hidden" name="liveagent.prechat.findorcreate.map.doCreate:Contact" value="LastName,true;FirstName,true;Email,true" />--> <input type="hidden" name="liveagent.prechat.findorcreate.map.doFind:Contact" value="LastName,true;FirstName,true;Email,true" /> <input type="hidden" name="liveagent.prechat.findorcreate.map.isExactMatch:Contact" value="LastName,true;FirstName,true;Email,true" /> <input type="hidden" name="liveagent.prechat.findorcreate.map.doCreate:Contact" value="LastName,true;FirstName,true;Email,true" /> <script type='text/javascript'> (function() { document.getElementById('closeInvite').onclick = function() { embedded_svc.inviteAPI.inviteButton.rejectInvite(); }; document.getElementById('rejectInvite').onclick = function() { embedded_svc.inviteAPI.inviteButton.rejectInvite(); }; // use this API call to reject invitations document.getElementById('acceptInvite').onclick = function() { embedded_svc.liveAgentAPI.startChat({ directToButtonRouting: { buttonId: "5733t000000cVk9" }, extraPrechatInfo: [], extraPrechatFormDetails: [] }); }; // use this API call to start chat from invitations document.addEventListener('keyup', function(event) { if (event.keyCode == 27) { embedded_svc.inviteAPI.inviteButton.rejectInvite(); }}) })(); </script> <!-- End of Invitations --> <script type='text/javascript' src='https://service.force.com/embeddedservice/5.0/esw.min.js'></script> <script type='text/javascript'> var initESW = function(gslbBaseURL) { embedded_svc.settings.displayHelpButton = true; //Or false embedded_svc.settings.language = ''; //For example, enter 'en' or 'en-US' embedded_svc.settings.defaultMinimizedText = 'Chat now'; //(Defaults to Chat with an Expert) embedded_svc.settings.disabledMinimizedText = 'Leave a message'; //(Defaults to Agent Offline) embedded_svc.settings.autoOpenPostChat = true; //embedded_svc.settings.loadingText = ''; //(Defaults to Loading) //embedded_svc.settings.storageDomain = 'yourdomain.com'; //(Sets the domain for your deployment so that visitors can navigate subdomains during a chat session) // Settings for Chat embedded_svc.settings.directToButtonRouting = function (prechatFormData) { if (prechatFormData[4].value === "Technical Service") return "5733t000000XZAM"; if (prechatFormData[4].value === "Customer Care") return "5733t000000XZAH"; }; embedded_svc.settings.prepopulatedPrechatFields = { OmniURL__c: window.location.href, ChooseaDepartment__c: 'Technical Service' }; //Sets the auto-population of pre-chat form fields embedded_svc.settings.extraPrechatFormDetails = [{ "label":"Source Domain", "value":window.location.href, "transcriptFields":[ "Source_Domain__c" ], "displayToAgent":true }]; //embedded_svc.settings.fallbackRouting = []; //An array of button IDs, user IDs, or userId_buttonId embedded_svc.settings.offlineSupportMinimizedText = 'Leave a message'; //(Defaults to Contact Us) 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type="text/javascript">window.NREUM||(NREUM={});NREUM.info={"beacon":"bam.nr-data.net","licenseKey":"NRJS-dd6144c4de227d09eb4","applicationID":"1022125825","transactionName":"YFxbZkpUXBYEVkYNWVkWbEBRGlsLAVBKSkZfSQ==","queueTime":0,"applicationTime":272,"atts":"TBtYEAJOTxg=","errorBeacon":"bam.nr-data.net","agent":""}</script></body> </html>

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