{"id":2447,"date":"2023-11-08T13:35:39","date_gmt":"2023-11-08T18:35:39","guid":{"rendered":"https:\/\/www.med.unc.edu\/microscopy\/?page_id=2447"},"modified":"2025-04-18T18:01:05","modified_gmt":"2025-04-18T22:01:05","slug":"kavli-nsi-idisco-workshop-2023-resource-list","status":"publish","type":"page","link":"https:\/\/www.med.unc.edu\/microscopy\/resources\/instructions-and-presentations\/kavli-nsi-idisco-workshop-2023-resource-list\/","title":{"rendered":"Kavli NSI iDISCO Workshop 2025 resource list"},"content":{"rendered":"<ul>\n<li>\n<h3>Tissue preparation<\/h3>\n<ul>\n<li><a href=\"https:\/\/idisco.info\/\" target=\"_blank\" rel=\"noopener\">Official iDISCO+ website (protocol, recommended antibodies, and more)<\/a><\/li>\n<li>AdipoClear:\n<ul>\n<li><a href=\"https:\/\/dx.doi.org\/10.3791\/58271\" target=\"_blank\" rel=\"noopener\">JOVE Video protocol<\/a><\/li>\n<li><a href=\"https:\/\/doi.org\/10.1016\/j.cmet.2017.12.011\" target=\"_blank\" rel=\"noopener\">Adipoclear research paper<\/a><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"https:\/\/www.med.unc.edu\/microscopy\/wp-content\/uploads\/sites\/1393\/2025\/04\/iDISCO_protocol_overview_and_troubleshooting.pdf\" target=\"_blank\" rel=\"noopener\">Tissue clearing tips and troubleshooting presentation<\/a> (courtesy of Alba Vieites Pardo)<\/li>\n<li><a href=\"https:\/\/www.sysy.com\/product\/226008\" target=\"_blank\" rel=\"noopener\">Recommended (rabbit) antibody for cFos mapping only [preferred]<\/a><\/li>\n<li><a href=\"https:\/\/www.sysy.com\/product\/226017\" target=\"_blank\" rel=\"noopener\">Recommended (rat) antibody for cFos mapping in combination with another antibody<\/a><\/li>\n<li>Lists of validated antibodies:\n<ul>\n<li><a href=\"https:\/\/idisco.info\/validated-antibodies\/\" target=\"_blank\" rel=\"noopener\">iDISCO+ website list of antibodies<\/a><\/li>\n<li><a href=\"https:\/\/mab3d-atlas.com\/\" target=\"_blank\" rel=\"noopener\">Zhuhao Wu&#8217;s database of validated monoclonal antibodies<\/a><\/li>\n<li><a href=\"https:\/\/www.miltenyibiotec.com\/US-en\/products\/macs-antibodies\/antibodies-for-microscopy-and-spatial-biology\/antibodies-for-3D-immunofluorescence.html?query=:relevance:Antibody-application:3D-Immunofluorescence\" target=\"_blank\" rel=\"noopener\">Miltenyi antibodies validated in light-sheet imaging<\/a><\/li>\n<li><a href=\"https:\/\/discotechnologies.org\/wildDISCO\/\" target=\"_blank\" rel=\"noopener\">Ali Erturk&#8217;s lab list of antibodies<\/a><\/li>\n<li><a href=\"https:\/\/transparent-human-embryo.com\/?page_id=634\" target=\"_blank\" rel=\"noopener\">Alain Chedotal&#8217;s lab list of antibodies for human embryos<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<li>\n<h3>Imaging<\/h3>\n<ul>\n<li><a href=\"https:\/\/www.med.unc.edu\/microscopy\/wp-content\/uploads\/sites\/1393\/2025\/04\/iDISCOworkshop2025_Ariel.pdf\" target=\"_blank\" rel=\"noopener\">Imaging cleared tissue with light-sheet microscopy<\/a><\/li>\n<li>UltraMicroscope II user guide: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/books\/NBK536385\/\" target=\"_blank\" rel=\"noopener\">HTML<\/a>, <a href=\"https:\/\/doi.org\/10.17615\/C69M15\" target=\"_blank\" rel=\"noopener\">PDF<\/a> (3D-printed holders at the bottom of the PDF download page)<\/li>\n<li>UltraMicroscope II video tutorials for <a href=\"https:\/\/youtube.com\/playlist?list=PL_P0beEBCtVLwlsNUeDVRzWhGHs17HhL4\" target=\"_blank\" rel=\"noopener\">usage<\/a> and <a href=\"https:\/\/youtube.com\/playlist?list=PL_P0beEBCtVLDKat4UpbExQhnM5eKQYPF\" target=\"_blank\" rel=\"noopener\">maintenance<\/a>.<\/li>\n<li><a href=\"https:\/\/www.med.unc.edu\/microscopy\/wp-content\/uploads\/sites\/1393\/2023\/11\/Light-sheet-instructions-Jul2020.pdf\" target=\"_blank\" rel=\"noopener\">UltraMicroscope II step-by-step instructions<\/a><\/li>\n<li><a href=\"https:\/\/www.med.unc.edu\/microscopy\/wp-content\/uploads\/sites\/1393\/2025\/04\/CLEARMAP-acquisition-settings-2025.docx\" target=\"_blank\" rel=\"noopener\">ClearMap and Tubemap suggested imaging settings<\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<h3>Visualization with Imaris Viewer and analysis with Imaris<\/h3>\n<ul>\n<li><a href=\"https:\/\/youtu.be\/kC8bNWKyHvc\" target=\"_blank\" rel=\"noopener\">Tutorial video for Imaris Viewer<\/a><\/li>\n<li><a href=\"https:\/\/imaris.oxinst.com\/homeschool\" target=\"_blank\" rel=\"noopener\">Tutorial videos for full version of Imaris<\/a><\/li>\n<\/ul>\n<\/li>\n<li>\n<h3>Visualization and analysis with Clearmap<\/h3>\n<ul>\n<li><a href=\"https:\/\/hackmd.io\/@talley\/SJB_lObBi#Python-environments-workshop\" target=\"_blank\" rel=\"noopener\">A fantastic guide to python environments (created by Talley Lambert, Harvard)<\/a> ; videos and slides version <a href=\"https:\/\/nic.med.harvard.edu\/python\/\" target=\"_blank\" rel=\"noopener\">here<\/a>.<\/li>\n<li><a href=\"https:\/\/www.med.unc.edu\/microscopy\/wp-content\/uploads\/sites\/1393\/2023\/11\/Installation-instructions-for-ClearMap-GUI-version-on-Linux.docx\" target=\"_blank\" rel=\"noopener\">[DEPRECATED] Installation instructions for Linux\u00a0 (working as of 20230504)<\/a><\/li>\n<li><a href=\"https:\/\/github.com\/ClearAnatomics\/ClearMap\" target=\"_blank\" rel=\"noopener\">Clearmap GitHub page<\/a><\/li>\n<li><a href=\"https:\/\/osf.io\/5qzn7\/\" target=\"_blank\" rel=\"noopener\">Original Clearmap test datasets from Renier lab (do not require stitching)<\/a><\/li>\n<li><a href=\"http:\/\/download.alleninstitute.org\/informatics-archive\/current-release\/mouse_ccf\/\" target=\"_blank\" rel=\"noopener\">Allen Brain Atlas download site<\/a><\/li>\n<li>Datasets from workshop (coming soon)<\/li>\n<\/ul>\n<\/li>\n<li>\n<h3>Data management<\/h3>\n<ul>\n<li><a href=\"https:\/\/www.med.unc.edu\/microscopy\/wp-content\/uploads\/sites\/1393\/2025\/04\/Data-transfer-considerations-UltraMicroscope-Blaze.pdf\" target=\"_blank\" rel=\"noopener\">Data transfer considerations for UltraMicroscope Blaze<\/a><\/li>\n<li><a href=\"https:\/\/www.med.unc.edu\/microscopy\/image\/hot-swap-drive-recommendations\/\" target=\"_blank\" rel=\"noopener\">Hot swap drive recommendations for UltraMicroscope II<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Tissue preparation Official iDISCO+ website (protocol, recommended antibodies, and more) AdipoClear: JOVE Video protocol Adipoclear research paper Tissue clearing tips and troubleshooting presentation (courtesy of Alba Vieites Pardo) Recommended (rabbit) antibody for cFos mapping only [preferred] Recommended (rat) antibody for cFos mapping in combination with another antibody Lists of validated antibodies: iDISCO+ website list of &hellip; <a href=\"https:\/\/www.med.unc.edu\/microscopy\/resources\/instructions-and-presentations\/kavli-nsi-idisco-workshop-2023-resource-list\/\" aria-label=\"Read more about Kavli NSI iDISCO Workshop 2025 resource list\">Read more<\/a><\/p>\n","protected":false},"author":58247,"featured_media":0,"parent":2560,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"layout":"","cellInformation":"","apiCallInformation":"","footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-2447","page","type-page","status-publish","hentry","odd"],"acf":[],"_links_to":[],"_links_to_target":[],"_links":{"self":[{"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/pages\/2447","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/users\/58247"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/comments?post=2447"}],"version-history":[{"count":8,"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/pages\/2447\/revisions"}],"predecessor-version":[{"id":3835,"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/pages\/2447\/revisions\/3835"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/pages\/2560"}],"wp:attachment":[{"href":"https:\/\/www.med.unc.edu\/microscopy\/wp-json\/wp\/v2\/media?parent=2447"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}