CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues

Stoltzfus, Caleb; Filipek, Jakub; Gern, Benjamin H.; Olin, Brandy E.; Leal, Joseph M.; Wu, Yajun; Lyons-Cohen, Miranda R; Huang, Jessica; Paz-Stoltzfus, Clarissa L.; Plumlee, Courtney R.; Pöschinger, Thomas; Urdahl, Kevin B.; Perro, Mario; Gerner, Michael Y.

doi:10.1016/j.celrep.2020.107523

Cited by 169 publications

(196 citation statements)

References 69 publications

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“…injection in order to keep EMOVI flexible and allow multiplexing of antibodies. Other recently published protocols demonstrated immunolabelling to detect structural components, neurons or vasculature in fixed organs ( 4 , 27 – 30 ); however, reports describing the detection of immune cells without the use of transgenic animals expressing cell-type specific fluorescent reporters remain rare ( 14 , 21 , 26 ). Our results demonstrated that EMOVI allows multiplexed antibody-based immunolabeling of immune cell populations in whole organs or large tissue pieces after fixation with the advantage of preserving fluorescence over several months.…”

Section: Discussionmentioning

confidence: 99%

“…However, EMOVI uses washing solution containing low concentrations of Triton-X 100, which further improves tissue penetrance along with de-lipidation ( 14 ). In addition to hyaluronidase treatment, we here often refrained from staining complete organs and instead used around 1mm thick organ slices or pieces to further improve antibody penetration into fixed organs, as has also been recommended by others ( 4 , 14 , 26 , 32 ). We found this type of sectioning crucial especially if aiming at homogenous staining for immune cell populations in organs such as the kidney, liver and heart.…”

Section: Discussionmentioning

confidence: 99%

“…Imaging immune cells in large-volume samples by confocal microscopy is a time-consuming process but provides a maximum of cellular resolution ( 14 , 21 , 26 ). To increase imaging speed, our results suggest that the widefield microscope with real-time computational clearing is a valuable and much faster alternative to confocal microscopy.…”

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Efficient Tissue Clearing and Multi-Organ Volumetric Imaging Enable Quantitative Visualization of Sparse Immune Cell Populations During Inflammation

et al. 2021

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Spatial information of cells in their tissue microenvironment is necessary to understand the complexity of pathophysiological processes. Volumetric imaging of cleared organs provides this information; however, current protocols are often elaborate, expensive, and organ specific. We developed a simplified, cost-effective, non-hazardous approach for efficient tissue clearing and multi-organ volumetric imaging (EMOVI). EMOVI enabled multiplexed antibody-based immunolabeling, provided adequate tissue transparency, maintained cellular morphology and preserved fluorochromes. Exemplarily, EMOVI allowed the detection and quantification of scarce cell populations during pneumonitis. EMOVI also permitted histo-cytometric analysis of MHC-II expressing cells, revealing distinct populations surrounding or infiltrating glomeruli of nephritic kidneys. Using EMOVI, we found widefield microscopy with real-time computational clearing as a valuable option for rapid image acquisition and detection of rare cellular events in cleared organs. EMOVI has the potential to make tissue clearing and volumetric imaging of immune cells applicable for a broad audience by facilitating flexibility in organ, fluorochrome and microscopy usage.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Efficient Tissue Clearing and Multi-Organ Volumetric Imaging Enable Quantitative Visualization of Sparse Immune Cell Populations During Inflammation

et al. 2021

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“…This is performed by an imaging approach that is linked to an analytical pipeline that can process the imaging data through an intuitive and interactive interface, which can provide quantitative outputs. Many such approaches have been described and have advantages and limitations (35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50). We recently reviewed such approaches and would refer the reader to these previous works (51,52).…”

Section: Available Methods To Assess Immune Cells Within the Kidney Amentioning

confidence: 99%

“…The output from tissue cytometry is expected to further increase, especially with advances in tissue clearing methods that allow mesoscale imaging (35,49,66).…”

Section: Future Outlook Challenges and Conclusionmentioning

confidence: 99%

Profiling Immune Cells in the Kidney Using Tissue Cytometry and Machine Learning

2022

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The immune system governs key functions that maintain renal homeostasis through various effector cells that reside in or infiltrate the kidney. These immune cells play an important role in shaping adaptive or maladaptive responses to local or systemic stress and injury. We increasingly recognize that microenvironments within the kidney are characterized by unique distribution of immune cells, the function of which depends on this unique spatial localization. Therefore, quantitative profiling of immune cells in intact kidney tissue becomes essential, particularly at a scale and resolution that allow the detection of differences between the various "nephro-ecosystems" in health and disease. In this review, we discuss advancements in tissue cytometry of the kidney, performed through multiplexed confocal imaging and analysis using the Volumetric tissue exploration and analysis (VTEA) software. We highlight how this tool has improved our understanding of the role of the immune system in the kidney and its relevance in pathobiology of renal disease. We also discuss how the field is increasingly incorporating machine learning to enhance the analytical potential of the imaging data and provide unbiased methods to explore and visualize multidimensional data. Such novel analytical methods could be particularly relevant when applied to profiling immune cells. Furthermore, machine learning approaches applied to cytometry could present venues for non-exhaustive exploration and classifications of cells from existing data and improving tissue economy. Therefore, tissue cytometry is transforming what used to be a qualitative assessment of the kidney into a highly quantitative imaging-based "omics" assessment that compliments other advanced molecular interrogation technologies.

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A Hitchhiker's guide through the bio‐image analysis software universe

et al. 2022

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Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualising information derived from microscopy imaging data of biological samples. In the past decade, we observed a dramatic increase in available software packages for these purposes. As it is increasingly difficult to keep track of the number of available image analysis platforms, tool collections, components and emerging technologies, we provide a conservative overview of software that we use in daily routine and give insights into emerging new tools. We give guidance on which aspects to consider when choosing the platform that best suits the user's needs, including aspects such as image data type, skills of the team, infrastructure and community at the institute and availability of time and budget.

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CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues

Cited by 169 publications

References 69 publications

Efficient Tissue Clearing and Multi-Organ Volumetric Imaging Enable Quantitative Visualization of Sparse Immune Cell Populations During Inflammation

Efficient Tissue Clearing and Multi-Organ Volumetric Imaging Enable Quantitative Visualization of Sparse Immune Cell Populations During Inflammation

Profiling Immune Cells in the Kidney Using Tissue Cytometry and Machine Learning

A Hitchhiker's guide through the bio‐image analysis software universe

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