{"id":3215,"date":"2021-07-16T17:13:09","date_gmt":"2021-07-16T21:13:09","guid":{"rendered":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/?page_id=3215"},"modified":"2026-02-10T11:15:16","modified_gmt":"2026-02-10T16:15:16","slug":"lightsheet-resources","status":"publish","type":"page","link":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/lightsheet-resources\/","title":{"rendered":"LightSheet"},"content":{"rendered":"<div id=\"pl-3215\"  class=\"panel-layout\" ><div id=\"pg-3215-0\"  class=\"panel-grid panel-no-style\" ><div id=\"pgc-3215-0-0\"  class=\"panel-grid-cell\" ><div id=\"panel-3215-0-0-0\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce panel-first-child\" data-index=\"0\" ><div class=\"textwidget\"><h2>Background<\/h2>\n<ul>\n<li><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2021\/07\/EN_special-edition_MA_Light-Sheet.pdf\" target=\"_blank\" rel=\"noopener\">Lightsheet Background Information <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/pmc.ncbi.nlm.nih.gov\/articles\/PMC10583220\/\" target=\"_blank\" rel=\"noopener\">Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2021\/07\/EN_41_011_058_LightsheetZ1_Sample-Preparation.pdf\" target=\"_blank\" rel=\"noopener\">Zeiss Lightsheet Sample Preparation <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2021\/07\/EN_41_013_093_QuickGuide_Lightsheet_Z1_for_Clearing.pdf\" target=\"_blank\" rel=\"noopener\">Zeiss Quick Guide: Imaging with Water or Clearing Immersion <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2021\/07\/EN_wp_Lightsheet-Z.1_Expanding-Clearing-Solutions.pdf\" target=\"_blank\" rel=\"noopener\">Zeiss Improved Imaging of Cleared Samples <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2024\/02\/ZeissInsightsTissueClearingImaging.pdf\" target=\"_blank\" rel=\"noopener\">Zeiss Insights into Tissue Clearing Imaging <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2021\/07\/EN_wp_refractive-index-clearing.pdf\" target=\"_blank\" rel=\"noopener\">Adjusting Refractive Index for Clearing Applications <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-content\/uploads\/sites\/149\/2022\/03\/wiley_zeiss-microscopy_the-art-of-tissue-clearing.pdf\" target=\"_blank\" rel=\"noopener\">Zeiss: The Art of Tissue Clearing <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"http:\/\/mesospim.org\/#\" target=\"_blank\" rel=\"noopener\">The mesoSPIM Initiative <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<\/div><\/div><div id=\"panel-3215-0-0-1\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce\" data-index=\"1\" ><div class=\"textwidget\"><h2>Reference Articles<\/h2>\n<ul>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC6168389\/\" rel=\"noopener\" target=\"_blank\">Clearing for Deep Tissue Imaging <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/s41596-021-00502-8\" target=\"_blank\" rel=\"noopener\">Tutorial: practical considerations for tissue clearing and imaging <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.biorxiv.org\/content\/10.1101\/2022.01.12.476113v1.full.pdf\" rel=\"noopener\" target=\"_blank\">EZ Clear for simple, rapid, and robust mouse whole organ clearing <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/27680942\/\" rel=\"noopener\" target=\"_blank\">Large-scale tissue clearing (PACT): Technical evaluation and new perspectives in immunofluorescence, histology, and ultrastructure <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fncel.2021.684792\/full\" rel=\"noopener\" target=\"_blank\">Passive Clearing and 3D Lightsheet Imaging of the Intact and Injured Spinal Cord in Mice <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/s41592-022-01632-x?utm_source=twitter&amp;utm_medium=social&amp;utm_campaign=nmeth\" target=\"_blank\" rel=\"noopener\">Practical Considerations for Quantitative Light Sheet Fluorescence Microscopy <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/s43586-021-00080-9?sap-outbound-id=7C293B1F8B9F606457EBD9EB22D075EC02A3D063&amp;utm_source=hybris-campaign&amp;utm_medium=email&amp;utm_campaign=110_MVM1398_0000026064_APSL_43586_AWA1_GL_PMLS_NEWLA_NRMP_SFN&amp;utm_content=EN_internal_48321_20221103&amp;mkt-key=42010A0550671EEA9BA362D653313E63\" target=\"_blank\" rel=\"noopener\">Tissue Clearing <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/23792946\/\" target=\"_blank\" rel=\"noopener\">SeeDB: A Simple and Morphology-preserving Optical Clearing Agent for Neuronal Circuit Reconstruction <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.nature.com\/articles\/s41422-018-0049-z\" target=\"_blank\" rel=\"noopener\">Tissue clearing of both hard and soft tissue organs with the PEGASOS method <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.protocols.io\/view\/lightsheetsampleprocessing-embryonicbrain-n2bvjy7nxvk5\/v1\" target=\"_blank\" rel=\"noopener\"><span>Lightsheet Sample Processing - Embryonic Brain<\/span> <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/li>\n<li><a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pmc\/articles\/PMC9214839\/\" target=\"_blank\" rel=\"noopener\">A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a> - reviews a variety of clearing techniques<\/li>\n<li>Ethyl Cinnamate Based Clearing\n<ul>\n<li>\n<p class=\"heading-title\"><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/30665888\/\" target=\"_blank\" rel=\"noopener\">Broad applicability of a streamlined ethyl cinnamate-based clearing procedure <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/p>\n<\/li>\n<li>\n<p class=\"heading-title\"><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/31620676\/\" target=\"_blank\" rel=\"noopener\">A network of trans-cortical capillaries as mainstay for blood circulation in long bones <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/p>\n<\/li>\n<li>\n<p class=\"heading-title\"><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/36430651\/\" target=\"_blank\" rel=\"noopener\">Optical Tissue Clearing to Study the Intra-Pulmonary Biodistribution of Intravenously Delivered Mesenchymal Stromal Cells and Their Interactions with Host Lung Cells <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a><\/p>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<\/div><\/div><div id=\"panel-3215-0-0-2\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce\" data-index=\"2\" ><div class=\"textwidget\"><h2>Specimen Holders<\/h2>\n<ul>\n<li>Overview of <a href=\"https:\/\/huiskenlab.com\/sample-mounting\/\" target=\"_blank\" rel=\"noopener\">sample mounting options from the Huisken Lab <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a>.<\/li>\n<li>Protocol for viewing <a href=\"https:\/\/www.jove.com\/v\/62741\/light-sheet-microscopy-of-fast-cardiac-dynamics-in-zebrafish-embryos\" target=\"_blank\" rel=\"noopener\">Zebrafish Embryos using light sheet microscopy <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a>.<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<\/div><\/div><div id=\"panel-3215-0-0-3\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce\" data-index=\"3\" ><div class=\"textwidget\"><h2>Industry Resources<\/h2>\n<p>Please note the refractive index when researching these products.<\/p>\n<ul>\n<li><a href=\"https:\/\/www.abcam.com\/kits\/tissue-clearing-methods-and-reagents?utm_source=Eloqua&amp;utm_medium=Email&amp;utm_campaign=Neuroscience%7cContent%7c42461%7cN%2FA%7cN%2FA%7cEng%7cAutomated%20-%20RA%20Nurture&amp;utm_content=Neuroscience%7c&amp;mi_u=724150\" rel=\"noopener\" target=\"_blank\" class=\"broken_link\">abcam  <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a>- Tissue clearing made easy<\/li>\n<li><a href=\"https:\/\/www.biolegend.com\/en-us\/3d-tissue-clearing?utm_source=newsletter&amp;utm_medium=Pardot&amp;utm_campaign=tuesday%20eblast&amp;utm_term=01%2F05\" rel=\"noopener\" target=\"_blank\">BioLegend <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a>- Ce3D Tissue Clearing<\/li>\n<li><a href=\"https:\/\/www.miltenyibiotec.com\/US-en\/products\/macs-imaging-solution.html#gref\" rel=\"noopener\" target=\"_blank\">Miltenyi Biotec - <\/a>MACS Imaging Solution<\/li>\n<li><a href=\"https:\/\/lifecanvastech.com\/products\/\" target=\"_blank\" rel=\"noopener\">LifeCanvas technologies <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a> - Tissue clearing reagents<\/li>\n<li><a href=\"https:\/\/www.translucencebio.com\/universal-tissue-clearing-kit\" target=\"_blank\" rel=\"noopener\">Translucence Biosystems <span class=\"sr-only\"> (opens in a new tab)<\/span><\/a> - Universal tissue clearing kit<\/li>\n<\/ul>\n<p>&nbsp;<\/p>\n<\/div><\/div><div id=\"panel-3215-0-0-4\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce\" data-index=\"4\" ><div class=\"textwidget\"><h2 id=\"clearing-methods\">Clearing Methods<\/h2>\n<table aria-describedby=\"clearing-methods\">\n<caption>\n    Comparison of tissue clearing methods, including refractive index, components,<br \/>\n    and optical performance. (T. Pratt, Zeiss)<br \/>\n  <\/caption>\n<thead>\n<tr>\n<th  scope=\"col\">Method<\/th>\n<th  scope=\"col\">Author<\/th>\n<th  scope=\"col\">RI<\/th>\n<th  scope=\"col\">Components<\/th>\n<th  scope=\"col\">LS Z.1<\/th>\n<th  scope=\"col\">Commnent<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td scope=\"row\">Scale A,B,U<\/td>\n<td >Miyawaki, Riken, JP<\/td>\n<td >1.38<\/td>\n<td >Glycerol, Urea, Triton<\/td>\n<td>+<\/td>\n<td>Alternative to BABB, less quenching, for myelinated tissue<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">CLARITY<\/td>\n<td>Chung and Deisseroth, Stanford, USA<\/td>\n<td>~1.45<\/td>\n<td>SDS PAGE and electrophoretic clearing<\/td>\n<td>++<\/td>\n<td>Very good results when it works, high failure rate (&gt; 50 %)<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">CUBIC<\/td>\n<td>Susaka et al, Riken, JP<\/td>\n<td>1.47- 1.49<\/td>\n<td>Optimized Scale<\/td>\n<td>++<\/td>\n<td>Published in Cell, April 2014<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">FocusClear<\/td>\n<td>CelExplorer Labs<\/td>\n<td>~1.45<\/td>\n<td>Commercial medium<\/td>\n<td>++<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">RapiClear<\/td>\n<td>CelExplorer Labs<\/td>\n<td>1.47 \u2013 1.55<\/td>\n<td>Based on FocusClear, more flexible in RI, cheaper<\/td>\n<td>+<\/td>\n<td>Comes in variants 1.47 \u2013 1.49 \u2013 1.52 - 155<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">TDE<\/td>\n<td>Hell et al, various labs tried<\/td>\n<td>Tunable<\/td>\n<td>97% 2,2\u2019-Thiodiethanol in water<\/td>\n<td>+<\/td>\n<td>TDE as mounting medium for different clearing (e.g. DMSO) , difficulties in reproducibility<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">LUMOS<\/td>\n<td>Efimova et al, Moscow<\/td>\n<td>1.45 - 1.47<\/td>\n<td>Not Known<\/td>\n<td>++<\/td>\n<td>Good results, some scattering left<br \/>\nCompatible with immunostainings, in situs and lipophilic tracer dyes<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">Glycerol\/H2O (80\/20)<\/td>\n<td>Generic<\/td>\n<td>1.45<\/td>\n<td>Simple mix of Glycerol and Water<\/td>\n<td>+<\/td>\n<td>Easy to reproduce, cheap<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">PACT, RIMS<\/td>\n<td>Bin Yang et al.<\/td>\n<td>1.45<\/td>\n<td>Perfusion assisted clearing,<\/td>\n<td>+<\/td>\n<td>Lab of Viviane Gradinaru<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div><\/div><div id=\"panel-3215-0-0-5\" class=\"so-panel widget widget_black-studio-tinymce widget_black_studio_tinymce panel-last-child\" data-index=\"5\" ><div class=\"textwidget\"><h2>Clearing Methods - Organic Solvent Based<\/h2>\n<p>The following clearing methods are organic solvent based and are not directly compatible with the Lightsheet Z.1 because they may damage the optical components. Samples may be protected by enclosing them in glass (Simax, refractive index 1.472), which enables use with a lightsheet system. See the associated white paper for expanding Simax-compatible clearing solutions when working with these organic solvents. (T. Pratt, Zeiss.)<\/p>\n<table>\n<thead>\n<tr>\n<th scope=\"col\">Method<\/th>\n<th scope=\"col\">Author<\/th>\n<th scope=\"col\">Refractive Index (RI)<\/th>\n<th scope=\"col\">Components<\/th>\n<th scope=\"col\">Comments<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td scope=\"row\">SeeDB<\/td>\n<td>Ke et al, JP<\/td>\n<td>1.47- 1.49<\/td>\n<td>Sucrose \/ Fructose saturated<\/td>\n<td>Very high viscosity sugar solutions, hard to get homogeneous medium, buoyancy of specimen, bubbles.<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">ClearT, ClearT2<\/td>\n<td>Kuwajima et al, 2013<\/td>\n<td>~1.45<\/td>\n<td>formamide\/ polyethylene glycol<\/td>\n<td>Formamide is highly corrosive, will damage dipping objectives<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">BABB<\/td>\n<td>Spalteholz 1914<\/td>\n<td>1.53-1.57<\/td>\n<td>Benzyl alcohol - Benzyl Benzoate<\/td>\n<td>Aka Murray\u2019s Clear, LSFM: Dodt, Stelzer, Giese<\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">Spalteholz<\/td>\n<td>Spalteholz 1914<\/td>\n<td>1.54<\/td>\n<td>Commercial medium<\/td>\n<td><\/td>\n<\/tr>\n<tr>\n<td scope=\"row\">3DISCO<\/td>\n<td>Erturk et al<\/td>\n<td>1.56<\/td>\n<td>developed starting from BABB; THF, DBE, DCM<\/td>\n<td>Fast and cheap clearing, fast fluorescent quenching<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"<p>Background Lightsheet Background Information (opens in a new tab) Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy (opens in a new tab) Zeiss Lightsheet Sample Preparation (opens in a new tab) Zeiss Quick Guide: Imaging with Water or Clearing Immersion (opens in a new tab) Zeiss Improved Imaging of Cleared Samples [&hellip;]<\/p>\n","protected":false},"author":283,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"publishpress_future_action":{"enabled":false,"date":"2026-04-16 19:37:38","action":"change-status","newStatus":"draft","terms":[],"taxonomy":""},"_links":{"self":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages\/3215"}],"collection":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/users\/283"}],"replies":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/comments?post=3215"}],"version-history":[{"count":61,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages\/3215\/revisions"}],"predecessor-version":[{"id":5083,"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/pages\/3215\/revisions\/5083"}],"wp:attachment":[{"href":"https:\/\/health.uconn.edu\/cell-analysis-modeling\/wp-json\/wp\/v2\/media?parent=3215"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}