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Image Tracing of Inflammatory Intestinal Organoids via Computational Clearing.

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Title: Image Tracing of Inflammatory Intestinal Organoids via Computational Clearing.
Authors: Jeon, Dong-Gyu1,2 (AUTHOR), Han, Min-Young2,3 (AUTHOR), Lee, Hana3,4 (AUTHOR), Hwang, Hanguk3,4 (AUTHOR), Lee, Ji-Min2,5 (AUTHOR), Kim, Eun Soo5,6 (AUTHOR), Lee, Gang Ho6,7 (AUTHOR), Chang, Yongmin1,3 (AUTHOR), Son, Mi-Young2,4 (AUTHOR), Park, Mae-Ja3,7 (AUTHOR), Nam, Sung-Wook1,2,3,4 (AUTHOR) nams@knu.ac.kr
Source: Nanomaterials (2079-4991). May2026, Vol. 16 Issue 10, p629. 19p.
Subjects: Fluorescence microscopy, Image enhancement (Imaging systems), Fluorimetry, RNA sequencing, Intestinal barrier function, Feature extraction, Dextran sulfate
Abstract: Computational clearing (CC) enhances widefield (WF) fluorescence microscopy by suppressing out-of-focus haze and autofluorescence, yielding semi-confocal quality images suitable for segmentation and image-based phenotyping. Here, we propose an "image tracing" workflow for inflammatory mouse intestinal organoids (mIOs) using paired CC and WF images to generate a differential signal (CC − WF). mIOs were derived from intestinal crypts of Lgr5-EGFP stem cell reporter mice and expanded under epidermal growth factor, Noggin, and R-spondin (ENR) conditions. Inflammation was induced by dextran sulfate sodium (DSS) treatment. CC processing enhanced phalloidin-stained apical F-actin and improved EGFP signals by reducing background noise, enabling robust segmentation and quantitative extraction of image morphometrics including area, circularity, and perimeter. CC-WF vectors derived from three-dimensional area–perimeter–circularity plots sensitively captured DSS-induced epithelial disruption analogous to a leaky-epithelium phenotype. Transcriptomic analysis by RNA-seq of DSS-treated mIOs revealed upregulation of inflammatory pathways including TNF-α signaling via NF-κB and IL-6/JAK/STAT3, aligning with microscopy findings. In a proof-of-concept demonstration using phalloidin-stained fluorescence images, ROC analysis of the CC-WF workflow achieved an AUC = 0.95 with 87.5% sensitivity and 92.9% specificity in distinguishing intact from injured mIOs. [ABSTRACT FROM AUTHOR]
Copyright of Nanomaterials (2079-4991) is the property of MDPI and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Image Tracing of Inflammatory Intestinal Organoids via Computational Clearing.
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  Data: <searchLink fieldCode="AR" term="%22Jeon%2C+Dong-Gyu%22">Jeon, Dong-Gyu</searchLink><relatesTo>1,2</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Han%2C+Min-Young%22">Han, Min-Young</searchLink><relatesTo>2,3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Lee%2C+Hana%22">Lee, Hana</searchLink><relatesTo>3,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Hwang%2C+Hanguk%22">Hwang, Hanguk</searchLink><relatesTo>3,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Lee%2C+Ji-Min%22">Lee, Ji-Min</searchLink><relatesTo>2,5</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Kim%2C+Eun+Soo%22">Kim, Eun Soo</searchLink><relatesTo>5,6</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Lee%2C+Gang+Ho%22">Lee, Gang Ho</searchLink><relatesTo>6,7</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Chang%2C+Yongmin%22">Chang, Yongmin</searchLink><relatesTo>1,3</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Son%2C+Mi-Young%22">Son, Mi-Young</searchLink><relatesTo>2,4</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Park%2C+Mae-Ja%22">Park, Mae-Ja</searchLink><relatesTo>3,7</relatesTo> (AUTHOR)<br /><searchLink fieldCode="AR" term="%22Nam%2C+Sung-Wook%22">Nam, Sung-Wook</searchLink><relatesTo>1,2,3,4</relatesTo> (AUTHOR)<i> nams@knu.ac.kr</i>
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  Data: <searchLink fieldCode="DE" term="%22Fluorescence+microscopy%22">Fluorescence microscopy</searchLink><br /><searchLink fieldCode="DE" term="%22Image+enhancement+%28Imaging+systems%29%22">Image enhancement (Imaging systems)</searchLink><br /><searchLink fieldCode="DE" term="%22Fluorimetry%22">Fluorimetry</searchLink><br /><searchLink fieldCode="DE" term="%22RNA+sequencing%22">RNA sequencing</searchLink><br /><searchLink fieldCode="DE" term="%22Intestinal+barrier+function%22">Intestinal barrier function</searchLink><br /><searchLink fieldCode="DE" term="%22Feature+extraction%22">Feature extraction</searchLink><br /><searchLink fieldCode="DE" term="%22Dextran+sulfate%22">Dextran sulfate</searchLink>
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  Label: Abstract
  Group: Ab
  Data: Computational clearing (CC) enhances widefield (WF) fluorescence microscopy by suppressing out-of-focus haze and autofluorescence, yielding semi-confocal quality images suitable for segmentation and image-based phenotyping. Here, we propose an "image tracing" workflow for inflammatory mouse intestinal organoids (mIOs) using paired CC and WF images to generate a differential signal (CC − WF). mIOs were derived from intestinal crypts of Lgr5-EGFP stem cell reporter mice and expanded under epidermal growth factor, Noggin, and R-spondin (ENR) conditions. Inflammation was induced by dextran sulfate sodium (DSS) treatment. CC processing enhanced phalloidin-stained apical F-actin and improved EGFP signals by reducing background noise, enabling robust segmentation and quantitative extraction of image morphometrics including area, circularity, and perimeter. CC-WF vectors derived from three-dimensional area–perimeter–circularity plots sensitively captured DSS-induced epithelial disruption analogous to a leaky-epithelium phenotype. Transcriptomic analysis by RNA-seq of DSS-treated mIOs revealed upregulation of inflammatory pathways including TNF-α signaling via NF-κB and IL-6/JAK/STAT3, aligning with microscopy findings. In a proof-of-concept demonstration using phalloidin-stained fluorescence images, ROC analysis of the CC-WF workflow achieved an AUC = 0.95 with 87.5% sensitivity and 92.9% specificity in distinguishing intact from injured mIOs. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
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  Data: <i>Copyright of Nanomaterials (2079-4991) is the property of MDPI and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – Type: doi
        Value: 10.3390/nano16100629
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      – Code: eng
        Text: English
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        PageCount: 19
        StartPage: 629
    Subjects:
      – SubjectFull: Fluorescence microscopy
        Type: general
      – SubjectFull: Image enhancement (Imaging systems)
        Type: general
      – SubjectFull: Fluorimetry
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      – SubjectFull: RNA sequencing
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      – SubjectFull: Intestinal barrier function
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      – SubjectFull: Feature extraction
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      – SubjectFull: Dextran sulfate
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      – TitleFull: Image Tracing of Inflammatory Intestinal Organoids via Computational Clearing.
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              Text: May2026
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