| _version_ | 1866902288335896576 |
|---|---|
| author | Srour, Salma |
| author_facet | Srour, Salma |
| contents | <p>This upload contains a CellProfiler pipeline (<code>.cppipe</code>, tested with CellProfiler v4.2.6) used to quantify nuclear and whole-cell features from fluorescence microscopy images for the associated manuscript [insert manuscript title/doi when available]. The workflow was <strong>adapted from published CellProfiler pipelines</strong>. Parameters were adjusted to suit this dataset. This record is provided solely to support transparency and reproducibility and <strong>does not claim original authorship of the underlying workflow.</strong> </p> <p><strong>Summary of workflow</strong></p> <ul> <li> <p><strong>Images/Metadata/NamesAndTypes/Groups:</strong> input configuration for batch processing.</p> </li> <li> <p><strong>IdentifyPrimaryObjects:</strong> segmentation of nuclei (DAPI).</p> </li> <li> <p><strong>IdentifySecondaryObjects:</strong> delineation of cell boundaries based on <strong>cytoplasmic protein</strong> staining.</p> </li> <li> <p><strong>MeasureObjectIntensity & MeasureImageIntensity:</strong> per-object and per-image intensity features.</p> </li> <li> <p><strong>Threshold & MaskObjects:</strong> background exclusion and ROI restriction.</p> </li> <li> <p><strong>MeasureObjectSizeShape:</strong> morphological features (size/shape).</p> </li> <li> <p><strong>ClassifyObjects:</strong> categorization of cells by whole-cell cytoplasmic-protein intensity.</p> </li> <li> <p><strong>ExportToSpreadsheet:</strong> export of measurements for downstream analysis (e.g., Excel/R).</p> </li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17194660 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Srour - Cell Profiler Pipeline Srour, Salma <p>This upload contains a CellProfiler pipeline (<code>.cppipe</code>, tested with CellProfiler v4.2.6) used to quantify nuclear and whole-cell features from fluorescence microscopy images for the associated manuscript [insert manuscript title/doi when available]. The workflow was <strong>adapted from published CellProfiler pipelines</strong>. Parameters were adjusted to suit this dataset. This record is provided solely to support transparency and reproducibility and <strong>does not claim original authorship of the underlying workflow.</strong> </p> <p><strong>Summary of workflow</strong></p> <ul> <li> <p><strong>Images/Metadata/NamesAndTypes/Groups:</strong> input configuration for batch processing.</p> </li> <li> <p><strong>IdentifyPrimaryObjects:</strong> segmentation of nuclei (DAPI).</p> </li> <li> <p><strong>IdentifySecondaryObjects:</strong> delineation of cell boundaries based on <strong>cytoplasmic protein</strong> staining.</p> </li> <li> <p><strong>MeasureObjectIntensity & MeasureImageIntensity:</strong> per-object and per-image intensity features.</p> </li> <li> <p><strong>Threshold & MaskObjects:</strong> background exclusion and ROI restriction.</p> </li> <li> <p><strong>MeasureObjectSizeShape:</strong> morphological features (size/shape).</p> </li> <li> <p><strong>ClassifyObjects:</strong> categorization of cells by whole-cell cytoplasmic-protein intensity.</p> </li> <li> <p><strong>ExportToSpreadsheet:</strong> export of measurements for downstream analysis (e.g., Excel/R).</p> </li> </ul> |
| title | Srour - Cell Profiler Pipeline |
| url | https://doi.org/10.5281/zenodo.17194660 |