Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool
Abstract Quantification of subcellular structures such as nuclei and cytoplasmic proteins using staining methods based on fluorescent dyes or fluorescently tagged antibodies are widely used in scientific research. Accurate high-throughput quantitation of these assays can be time consuming and challe...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-025-12144-x |
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| author | Lucas Unger Ulrik Larsen Shayla Sharmine Md Kaykobad Hossain Thomas Aga Legøy Marc Vaudel Luiza Ghila Simona Chera |
| author_facet | Lucas Unger Ulrik Larsen Shayla Sharmine Md Kaykobad Hossain Thomas Aga Legøy Marc Vaudel Luiza Ghila Simona Chera |
| author_sort | Lucas Unger |
| collection | DOAJ |
| description | Abstract Quantification of subcellular structures such as nuclei and cytoplasmic proteins using staining methods based on fluorescent dyes or fluorescently tagged antibodies are widely used in scientific research. Accurate high-throughput quantitation of these assays can be time consuming and challenging. Here, we present our FIJI based Semi-Automated counting Macro termed SAM, and we validate its accuracy against manual counting and other automated counting methods. By introducing this automated quantification tool, we aim to contribute to the ongoing efforts to enhance the reliability, efficiency, and standardization of immunostaining analysis in the field of diabetes research and beyond. |
| format | Article |
| id | doaj-art-d7d0f48fdbb845b281a6a7255e769b1e |
| institution | DOAJ |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-d7d0f48fdbb845b281a6a7255e769b1e2025-08-20T03:04:29ZengNature PortfolioScientific Reports2045-23222025-07-0115111110.1038/s41598-025-12144-xEfficient cytoplasmic cell quantification using a semi-automated FIJI-based toolLucas Unger0Ulrik Larsen1Shayla Sharmine2Md Kaykobad Hossain3Thomas Aga Legøy4Marc Vaudel5Luiza Ghila6Simona Chera7Mohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of BergenMohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of BergenMohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of BergenDepartment of Clinical Science, Faculty of Medicine, University of BergenMohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of BergenMohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of BergenMohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of BergenMohn Research Center for Diabetes Precision Medicine, Department of Clinical Science, Faculty of Medicine, University of BergenAbstract Quantification of subcellular structures such as nuclei and cytoplasmic proteins using staining methods based on fluorescent dyes or fluorescently tagged antibodies are widely used in scientific research. Accurate high-throughput quantitation of these assays can be time consuming and challenging. Here, we present our FIJI based Semi-Automated counting Macro termed SAM, and we validate its accuracy against manual counting and other automated counting methods. By introducing this automated quantification tool, we aim to contribute to the ongoing efforts to enhance the reliability, efficiency, and standardization of immunostaining analysis in the field of diabetes research and beyond.https://doi.org/10.1038/s41598-025-12144-x |
| spellingShingle | Lucas Unger Ulrik Larsen Shayla Sharmine Md Kaykobad Hossain Thomas Aga Legøy Marc Vaudel Luiza Ghila Simona Chera Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool Scientific Reports |
| title | Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool |
| title_full | Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool |
| title_fullStr | Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool |
| title_full_unstemmed | Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool |
| title_short | Efficient cytoplasmic cell quantification using a semi-automated FIJI-based tool |
| title_sort | efficient cytoplasmic cell quantification using a semi automated fiji based tool |
| url | https://doi.org/10.1038/s41598-025-12144-x |
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