Organoid Clearing
Organoid Clearing - Related Videos
05:11
Organoid Electroporation: A Method to Transfect Plasmid DNA into Gastrointestinal Organoids
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2023
This video describes the electroporation protocol for transfecting large plasmids into three-dimensional gastrointestinal organoids to prove its universal functionality in different entities, namely pancreatic ductal adenocarcinoma (PDAC), colorectal cancer (CRC), cholangiocarcinoma (CCC), and gastric cancer (GC) organoids.
03:41
CRC Organoid Culture: A Method to Obtain 3D Organoids from Colorectal Cancer Cells
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2023
This video describes the detailed protocol for generating 3D organoids from murine-model derived colorectal cancer cells by propagating them on artificial extracellular matrix coated plates. These CRC organoids can be used as a model to study the primary growth of human tumor cells and metastasis.
10:03
Multiphoton Microscopy of Cleared Mouse Brain Expressing YFP
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Cited by 11 •
2012
Multiphoton microscopy of whole mouse organs is possible by optically clearing the organ before imaging, but not all protocols preserve the fluorescent signal of fluorescent proteins. Using an optical clearing method with ethanol-based dehydration and benzyl alcohol:benzyl benzoate clearing, we show high-resolution multiphoton images of whole mouse brain expressing YFP.
10:30
Organoids as Model for Infectious Diseases: Culture of Human and Murine Stomach Organoids and Microinjection of Helicobacter Pylori
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Cited by 144 •
2015
Stem cell derived cultures harbor tremendous potential to model infectious diseases. Here, the culture of mouse and human gastric organoids derived from adult stem cells is described. The organoids are microinjected with the gastric pathogen Helicobacter pylori.
08:25
Analysis of Coronary Vessels in Cleared Embryonic Hearts
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Cited by 11 •
2016
We present a protocol for the analysis of coronary vessels in whole embryonic murine hearts up to E15.5, using standard immunological staining methods followed by optical clearance and confocal microscopy. This technique enables visualization of blood vessels throughout the entire heart without the need for time-consuming analysis of serial sections.
FAQs
Chemical treatment targets light-scattering components, particularly lipids, by removing them or modifying their optical contribution. Refractive-index matching then reduces differences in how light travels through the organoid. Together, these changes improve optical access to internal regions, which is essential for mapping structures throughout a three-dimensional model.
Matching refractive indices across the sample reduces optical differences between its components, helping light pass through regions that would otherwise scatter it. This step works alongside lipid removal or modification rather than replacing it: chemical treatment addresses scattering sources, while index matching improves optical uniformity. The combined effect supports more consistent visualization of internal morphology during microscopy.
Fluorescent labels and genetically encoded reporters can retain cellular signals during preparation, allowing optical imaging to be linked with biological identity. Those signals help researchers distinguish cell types and examine morphology, growth patterns, and spatial interactions within the same three-dimensional model. This combination allows structural observations to be interpreted alongside cell-specific or molecular information.
Keeping the organoid intact preserves relationships among cells and structures across the full three-dimensional model, rather than restricting analysis to separated slices. Imaging can therefore reveal spatial interactions, overall growth patterns, and the organization of internal morphology in their original context. For biology studies, this supports a more complete connection between architecture and cellular readouts.
A basic workflow begins with chemical treatment that removes or modifies light-scattering components and adjusts refractive indices across the sample. Fluorescent labels or genetically encoded reporters provide signals for cellular interpretation, after which the cleared organoid is examined with confocal or light-sheet microscopy. Researchers can then map cell types, morphology, growth patterns, and spatial interactions throughout the model.
It is useful when a study needs three-dimensional information from a complex organoid phenotype. Applications supported by the method include developmental biology, disease modeling, drug studies, and quantitative analysis. Depending on the biological question, researchers can assess cell types, morphology, growth patterns, or spatial interactions, connecting these measurements to the intact architecture of the model.